# libraries used for analysis
library(edgeR)
library(limma)
library(quadprog)
library(ruv)
# libraries required for graphics
library(ggplot2)
library(reshape2)
library(EDASeq)
library(RColorBrewer)
library(VennDiagram)
library(data.table)
library(dplyr)
library(stringr)
library(knitr)
library(pheatmap)
wd = "./"
colors <- c("#0571b0", "#ca0020")
We first produce a matrix of read counts after aligning to both the Human and Plasmodium falciparum 3D7 reference genome. Subread’s featureCounts program is then used to allocate reads to gene features using the gff file PlasmoDB-12.0_Pfalciparum3D7.gff from PlasmoDB. For both Subread programs the default options are used.
setwd(wd)
# # Next subreads featureCounts was used to allocate reads to genes. This
# was saved for re-use files <-
# Sys.glob('/home/users/allstaff/tonkin-hill.g/all_gene_analysis/alignment/*.sam')
# fc_genes_aligned_w_Pfhuman_withoutVivax <- featureCounts(files, annot.ext
# = './data/PlasmoDB-12.0_Pfalciparum3D7.gff' , isPairedEnd=TRUE,
# isGTFAnnotationFile=TRUE, GTF.attrType='ID', GTF.featureType='gene' ,
# nthreads=15)
# Load gene ID mappings which we use later on.
geneID_mappings <- fread("./data/geneID_mappings.txt", data.table = FALSE, stringsAsFactors = FALSE)
trim <- function(x) gsub("^\\s+|\\s+$", "", x)
s <- str_split(as.character(geneID_mappings$`[Previous ID(s)]`), ",")
geneID_mappings <- data.frame(current = rep(geneID_mappings$`[Gene ID]`, sapply(s,
FUN = length)), old = unlist(s))
geneID_mappings$old <- str_trim(geneID_mappings$old)
# Load read counts (if featureCounts has been run previously)
load("./data/fc_genes_with_all_samples_aligned_human_Pf_WithOutVivax_subread_uH.RData")
fc2 <- fc_genes_aligned_w_Pfhuman_withoutVivax
t <- fc2$counts
# Rename samples to something more sensible colnames(t) <-
# gsub('alignment\\.sam','',colnames(t)) colnames(t) <-
# gsub('.*vivax\\.','',colnames(t)) colnames(t) <- gsub('_S.*','',
# colnames(t))
fc2$counts <- t
x <- DGEList(counts = fc2$counts, genes = fc2$annotation)
We next filter out genes that do not have sufficient coverage across our samples for reliable estimates to be made.
setwd(wd)
before <- nrow(x$counts)
keep <- rowSums(cpm(x) > 2) >= 10
x <- x[keep, , keep.lib.sizes = FALSE]
We require that there are at least 2 reads per million for at least 10 samples in order for a gene to be included in the analysis. This reduced the number of genes being considered from 5777 to 4144.
setwd(wd)
bplot <- melt(colSums(x$counts))
colnames(bplot) <- c("Read.Counts")
bplot$Sample <- rownames(bplot)
gg <- ggplot(bplot, aes(x = factor(Sample), y = Read.Counts)) + geom_bar(stat = "identity")
gg <- gg + theme_bw() + scale_y_sqrt(breaks = c(0, 10000, 1e+06, 1e+07, 1e+08))
gg <- gg + theme(axis.text.x = element_text(size = 12, angle = 90), axis.text.y = element_text(size = 12,
angle = 0), axis.title = element_text(size = 14, face = "bold"))
gg <- gg + labs(x = "Sample", y = "Read Count")
gg <- gg + geom_hline(aes(yintercept = 1e+06), col = "red")
x$counts <- x$counts[, !grepl("SFD1|SFM9|SFC\\.025", colnames(x$counts))]
filt.annnotation <- fc2$annotation[fc2$annotation$GeneID %in% rownames(x$counts),
]
dge <- DGEList(counts = x$counts, genes = filt.annnotation)
gg
Samples SFD1, SFM9 and SFC.025 were not sequenced to a sufficient depth to be reliable and thus are removed.
Samples SFU2 and SFU3 were drug treated and are removed.
x$counts <- x$counts[, !grepl("SFU2|SFU\\.3", colnames(x$counts))]
filt.annnotation <- fc2$annotation[fc2$annotation$GeneID %in% rownames(x$counts),
]
dge <- DGEList(counts = x$counts, genes = filt.annnotation)
Now we take the log transform of our sample counts (RPKM) to estimate the proportion of different stages present.
setwd(wd)
our_log_rpkm <- rpkm(dge)
our_log_rpkm <- log2(1 + our_log_rpkm)
To estimate the proportion of different life-cycle stages in each of our samples we require a reference data set. Su et al provide such a reference. They performed RNA-seq at two gametocyte stages, an ookinete stage and four time points of erythrocytic stages representing ring, early trophozoite, late trophozoite, and schizont. As we do not expect any ookinete stage parasites we discarded this reference. The data was downloaded from PlasmoDB and as such read counts were reported in RPKM. To handle outlying counts in a sensible manner a log2 transformation of the RPKM values was performed. This was also done for our gene counts. By next fitting a mixture model we can estimate the proportion of different parasite stages that make up our samples.
setwd(wd)
su_rpkm <- read.csv("./data/ rpkm_7SexualAndAsexualLifeStages_suetal.csv", header = TRUE,
sep = ",")
# ignore the Ookinete profile as this should be absent from our data.
su_rpkm$Ookinete <- NULL
rownames(su_rpkm) <- su_rpkm$ID
su_rpkm$ID <- NULL
# take the log transform of the data which helps to manage outlier genes.
su_log_rpkm <- log2(1 + su_rpkm)
Given a set of stages \(S\) and a set of genes \(g_i: i\in \{1,...,N\}\) we want to minimise
\[ \sum_{i=1}^N \left( g_{i,sample} - \sum_{s \in S} \pi_s g_{i,s} \right)^2 \]
Subject to constraints
\[ \sum_{s\in S} \pi_s = 1 \]
\[ \pi_s > 0 \]
Here \(\pi_s\) is proportion of stage \(s\) that is attributed to having contributed to our sample. This model was fit using R’s solve.QP function.
setwd(wd)
findMix <- function(Y, X) {
X[is.na(X)] <- t(replicate(ncol(X), apply(X, 1, mean, na.rm = T)))[is.na(X)]
Rinv <- solve(chol(t(X) %*% X))
C <- cbind(rep(1, ncol(X)), diag(ncol(X)))
b <- c(1, rep(0, ncol(X)))
d <- t(Y) %*% X
qp <- solve.QP(Dmat = Rinv, factorized = TRUE, dvec = d, Amat = C, bvec = b,
meq = 1)
sol <- qp$solution
sol[sol < 1e-10] <- 0
return(sol)
}
We fit this mixture model to each of our samples in turn. The results are then plotted. A column represents each sample in the plot below. As we are fitting proportion parameters each columns values must add to 1 over the 5 stages. Note that we have also combined the estimated proportions for the gametocyte samples into one gametocyte variable. The columns are coloured by phenotype.
setwd(wd)
# First get the intersection of the genes for the two datasets and order
# them by rowname.
inter <- intersect(rownames(our_log_rpkm), rownames(su_log_rpkm))
O <- our_log_rpkm[rownames(our_log_rpkm) %in% inter, ]
O <- O[order(rownames(O)), ]
S <- su_log_rpkm[rownames(su_log_rpkm) %in% inter, ]
S <- S[order(rownames(S)), ]
# Now lets fit some samples!
ourPlotData <- data.frame()
for (i in 1:ncol(O)) {
mix <- findMix(O[, i], as.matrix(S))
ourPlotData <- rbind(ourPlotData, data.frame(sample = rep(colnames(O)[i],
ncol(S)), stage = colnames(S), proportion = mix))
}
# Organise the results.
ourPlotData$stage <- gsub("Gametocyte.*", "Gametocyte", ourPlotData$stage)
ourPlotData <- aggregate(proportion ~ sample + stage, data = ourPlotData, FUN = sum)
ourPlotData <- within(ourPlotData, stage <- factor(stage, levels = c("Ring",
"Early.Trophozoite", "Late.Trophozoite", "Schizont", "Gametocyte")))
ourPlotData$phenotype <- ifelse(substring(ourPlotData$sample, 1, 1) == "I",
"non-severe", "severe")
# Make a pretty plot.
gg <- ggplot(ourPlotData, aes(x = factor(sample), y = proportion, fill = factor(phenotype))) +
geom_bar(stat = "identity")
gg <- gg + scale_fill_manual(values = c(`non-severe` = "#2c7bb6", severe = "#d7191c"))
gg <- gg + facet_wrap(~stage, ncol = 1)
gg <- gg + theme_bw()
gg <- gg + theme(axis.text.x = element_text(size = 12, angle = 90), axis.text.y = element_text(size = 12,
angle = 0), axis.title = element_text(size = 14, face = "bold"), strip.text.x = element_text(size = 16,
face = "bold"))
gg <- gg + labs(x = "Sample", y = "Proportion", fill = "Stage")
gg <- gg + theme(legend.text = element_text(size = 14))
gg <- gg + theme(legend.key.size = unit(0.25, "in"))
gg <- gg + theme(legend.title = element_text(size = 16, face = "bold"))
gg <- gg + guides(fill = guide_legend(title = "Phenotype"))
gg
We now perform the Voom transformation on our count matrix. Prior to the transformation we use TMM normalisation to account for the different library sizes present in our sample. TMM was chosen as it is more robust to outliers. From the Voom variance trend it is evident that there are a number of genes that have both high variability and high expression. After looking at some of the main offenders these were identified to be influenced by staging in the parasite. Consequently it is important to account for life-cycle stage when conducting the differential expression analysis.
options(width = 150)
setwd(wd)
categories <- as.factor(substring(rownames(dge$samples), 1, 1))
dge <- calcNormFactors(dge, method = "TMM")
dge$samples$group <- categories
design <- model.matrix(~group, data = dge$samples)
v <- voom(dge, design = design, plot = TRUE)
The PCA plot below indicates that accounting for library size alone does not cope with the impact of life-cycle stages. Notably SFC21 is clearly an outlier and was identified in the mixture model as containing later stage parasites as well as gametocytes. IFM14 is also slightly separate in the PCA plot and was identified as having a proportion of Schizont stage parasite present.
setwd(wd)
plotPCA(v$E, col = colors[categories], cex = 0.8, isLog = TRUE)
Further the Relative Log Expression (RLE) plot below suggests that there is something different about SFC21 as well as highlighting IFM060 as being different.
setwd(wd)
plotVoomRLE <- function(E, colours) {
mn <- apply(E, 1, median)
rle <- data.frame(sweep(E, MARGIN = 1, STATS = mn, FUN = "-"))
boxplot(rle, col = colours, outline = FALSE, las = 2, ylim = c(-7, 7))
abline(h = 0, col = "black")
}
plotVoomRLE(v$E, colors[categories])
To investigate the impact of life-cycle stages in our analysis we fit a linear model using limma’s removeBatchEffect. Initially ring, gametocyte and schizont parameters were fit along with the disease phenotype factor. This was because for the most part the Trophozoite stages could be represented by accounting for these stages as they would be present implicitly in the model.
The PCA indicates that we have dealt with the outlying SFC21 sample as well as other less outlying samples such as IFM14 which showed a proportion of Schizont stage parasites in the mixture model. Unfortunately due to the low number of samples that have proportions of Schizont and Gametocytes estimating differential differential expression in severe disease becomes impossible. This is because there is insufficient data to estimate these stage parameters and consequently the uncertainty in the model is too high to find significant differences between severe and non-severe disease.
setwd(wd)
covs <- data.frame(v$design[, 2])
ourPlotData$phenotype <- NULL
c <- dcast(ourPlotData, sample ~ ..., value.var = "proportion")
covs <- merge(covs, c, by.x = 0, by.y = "sample")
colnames(covs) <- c("sample", "disease", colnames(c)[2:ncol(c)])
rownames(covs) <- covs$sample
covs$sample <- NULL
covs <- covs[match(colnames(v$E), rownames(covs)), ]
stopifnot(colnames(v$E) == rownames(covs))
# head(covs)
covs <- covs[, c(1, 2, 5, 6)]
# head(covs)
mod = model.matrix(as.formula(paste("~", paste(colnames(covs), collapse = " + "), sep = "")), data = covs)
norm_counts_ring <- removeBatchEffect(v$E, covariates = mod[, 3:ncol(mod)], design = mod[, 1:2])
plotPCA(norm_counts_ring, col = colors[categories], cex = 0.8, isLog = TRUE)
The RLE plot also suggests we have dealt with SFC21 however accounting for these stages does not seem to have accounted for the differences we see in the IFM060 sample. The mixture model did not identify IFM060 as being noticeably different from the other samples and consequently it is likely that there is some other unknown factor impacting on its expression.
setwd(wd)
plotVoomRLE(norm_counts_ring, col = colors[categories])
We then investigate the impact of only accounting for the Ring stage parameter in the model. This gives us more power with which to identify differential expression related to severe disease. However, from the PCA plot below it is clear that accounting for Ring stage alone is insufficient and fails to adequately deal with SFC21.
setwd(wd)
covs <- covs[, c(1, 2)]
mod = model.matrix(as.formula(paste("~", paste(colnames(covs), collapse = " + "), sep = "")), data = covs)
norm_counts_ring <- removeBatchEffect(v$E, covariates = mod[, 3:ncol(mod)], design = mod[, 1:2])
plotPCA(norm_counts_ring, col = colors[categories], cex = 0.8, isLog = TRUE)
We are however able to identify differentially expressed genes in this less parameterised model. The summary of results accounting only for the Ring stage variable are given below. This test was performed using the limma-Voom pipeline. Ideally we would be able to keep both the power in out tests and account for the remaining unwanted factors. To achieve this we make use of RUV-4 to estimate dummy variables that represent multiple unknown factors of unwanted variation.
setwd(wd)
stopifnot(colnames(dge) == rownames(mod))
v2 <- voom(dge, design = mod, plot = FALSE)
fit <- lmFit(v2, mod)
fit <- eBayes(fit, robust = TRUE)
summary(de1 <- decideTests(fit, adjust.method = "BH", p.value = 0.05))
## (Intercept) disease Ring
## -1 85 58 1295
## 0 645 3939 1672
## 1 3414 147 1177
To cope with the outlier samples such as SFC21 whilst retaining statistical power we estimate factors of unwanted variation using RUV-4.
RUV-4 requires a set of control genes which are believed to be relatively unaffected by the condition of interest, in our case this is disease severity. RUV-4 is however fairly robust to the choice of control genes.
We chose to use the 1000 genes found to have the highest p-values in the experiment of Vignali et al as controls. The experiment of Vignali et al looked at differences in expression between pregnancy associated malaria and childhood malaria. Although this is not the same association we are investigating it was considered close enough to perform adequately as a source of control genes. Further an analysis using SVA which does not require controls and rather estimates them empirically was found to produce similar results with only 5 out of 119 genes found using SVA missing from the RUV-4 approach. Further RUV-4 attempts to recover some variation that may be lost in the vanilla SVA approach when the factor of interest (severe disease) correlates with an unwanted factor. Consequently it leads to a higher number of differentially expressed genes being found. It was also thought that having an independently sourced set of control genes was preferable to empirically deriving such a set.
setwd(wd)
contol_genes_vignali <- read.table("./data/contol_genes_vignali.txt", quote = "\"")
ctrl_vignali <- geneID_mappings$current[geneID_mappings$old %in% contol_genes_vignali$V1]
length(ctrl_vignali)
## [1] 1009
empirical_controls <- ctrl_vignali[0:length(ctrl_vignali)]
empirical_controls <- rownames(v$E) %in% empirical_controls
categoriesRUV <- categories
categoriesRUV <- data.matrix(as.numeric(categoriesRUV == "S"))
ring <- data.matrix(mod[, c(1, 3)])
genes <- data.matrix(t(v$E))
ruv <- RUV4(genes, categoriesRUV, empirical_controls, 3, Z = ring)
modRUV = cbind(mod, ruv$W)
norm_counts_ring_ruv <- removeBatchEffect(v$E, covariates = modRUV[, 3:ncol(modRUV)], design = modRUV[, 1:2])
Note that although we used 1000 genes from the experiment of Vignali et al only 533 were found in our reduced expression matrix.
The PCA plot below indicates that we have dealt with most of the problems due to staging. Here we have included the Ring stage proportion from the mixture model as well as three factors of unwanted variation estimated using RUV-4.
setwd(wd)
plotPCA(norm_counts_ring_ruv, col = colors[categories], cex = 0.8, isLog = TRUE)
The RLE plot also indicates that we have succesfully dealt with most of the staging issues. Both SFC21 and IFM14 have reasonable box plots. Moreover, IFM060 has a nicer boxplot indicating that in using RUV-4, not only have we dealt with staging issues, we have also accounted for some other unknown confounding factors that would have impacted our results. The variation in each sample has also been reduced which is indicated in the reduced height of the boxplot whiskers. Finally, the results were found to be relatively robust to the removal of the outlier samples such as SFC21 and IFM14. Consequently, this approach seems to succesfully deal with both life-cycle staging issues and other unknown impacting factors.
setwd(wd)
plotVoomRLE(norm_counts_ring_ruv, colors[categories])
We now use the limma-voom pipeline, with the robust ebayes option which handles dispersion outliers. This was done to further ensure our results were less likely to be affected by outlier samples. Multiple testing correction was performed using the Benjamini-Hochberg approach.
setwd(wd)
stopifnot(colnames(dge) == rownames(modRUV))
v2 <- voom(dge, design = modRUV, plot = F)
fit <- lmFit(v2, modRUV)
fit <- eBayes(fit, robust = TRUE)
s <- summary(de2 <- decideTests(fit, adjust.method = "BH", p.value = 0.05))
s
## (Intercept) disease Ring
## -1 94 153 1391 1682 1143 545
## 0 521 3873 1429 1579 1870 2954
## 1 3529 118 1324 883 1131 645
Overall 271 genes were found to be differentially expressed between severe and non-severe cases of malaria with a false dicovery rate threshold of 0.05.
A good check for validity of our model it to look at the distribution of the resulting p-values. If everything is okay we would expect a uniform distribution except near \(p=0\) where we would hope to see a spike. The barplot below indicates this is what we see which is helpful in affirming that we have done okay in removing unwanted variation without negatively impacting on the variation due to the variable of interest (diseas severity).
setwd(wd)
top_ring_ruv <- topTable(fit, coef = 2, p.value = 0.1, sort.by = "p", number = Inf, adjust.method = "BH", confint = TRUE)
hist <- data.frame(topTable(fit, coef = 2, number = Inf))
gg <- ggplot(hist, aes(x = P.Value)) + geom_histogram(binwidth = 0.01)
gg <- gg + theme_bw()
gg <- gg + theme(axis.text.x = element_text(size = 12), axis.text.y = element_text(size = 12, angle = 0), axis.title = element_text(size = 12, face = "bold"))
gg <- gg + labs(x = "P value", y = "Count")
gg
Below is a table of genes that were found to be differentially expressed, ordered by their respective p-values. The 95% confidence intervals are given with the estimated LFC as well as the BH adjusted p-values and the log-odds that the gene is differentially expressed. Here we report for interest sake all genes up to a adjusted p-value threshold of 0.1.
setwd(wd)
# Load additional gene information
GeneAnnotationPlasmoDB <- fread("./data/GeneAnnotationPlasmoDB.txt", data.table = FALSE, na.strings = "N/A")
# First lets import some additional gene information to make a nicer table
GeneAnnotationPlasmoDB <- GeneAnnotationPlasmoDB[, colnames(GeneAnnotationPlasmoDB) %in% c("[Gene ID]", "[Product Description]", "[Gene Name or Symbol]")]
top_ring_ruv <- merge(top_ring_ruv, GeneAnnotationPlasmoDB, by.x = 0, by.y = "[Gene ID]", all.x = TRUE)
top_ring_ruv <- top_ring_ruv[with(top_ring_ruv, order(adj.P.Val)), ]
# Now print the table
top_ring_ruv$P.Value <- format(top_ring_ruv$P.Value, scientific = TRUE, digits = 3)
top_ring_ruv$adj.P.Val <- format(top_ring_ruv$adj.P.Val, scientific = TRUE, digits = 3)
kable(top_ring_ruv[, c(2:4, 6:ncol(top_ring_ruv))], digits = 3)
| GeneID | Chr | Start | Strand | Length | logFC | CI.L | CI.R | AveExpr | t | P.Value | adj.P.Val | B | [Product Description] | [Gene Name or Symbol] | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 15 | PF3D7_0202000 | Pf3D7_02_v3 | 103385 | - | 2412 | -2.278 | -2.637 | -1.918 | 14.110 | -6.254 | 3.21e-07 | 1.33e-03 | 6.653 | knob-associated histidine-rich protein | KAHRP |
| 55 | PF3D7_0400100 | Pf3D7_04_v3 | 28706 | + | 8972 | -1.593 | -2.375 | -0.811 | 4.842 | -5.412 | 3.06e-06 | 6.35e-03 | 4.487 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 11 | PF3D7_0115700 | Pf3D7_01_v3 | 607390 | - | 7504 | -1.460 | -2.203 | -0.718 | 4.616 | -4.768 | 2.42e-05 | 9.51e-03 | 2.581 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 43 | PF3D7_0316600 | Pf3D7_03_v3 | 669302 | - | 1572 | -1.586 | -1.920 | -1.251 | 10.261 | -5.022 | 1.30e-05 | 9.51e-03 | 3.090 | formate-nitrite transporter | FNT |
| 132 | PF3D7_0532400 | Pf3D7_05_v3 | 1312471 | + | 1684 | -1.578 | -2.148 | -1.008 | 8.158 | -4.801 | 2.53e-05 | 9.51e-03 | 2.485 | lysine-rich membrane-associated PHISTb protein | LyMP |
| 133 | PF3D7_0600600 | Pf3D7_06_v3 | 29618 | - | 1867 | -1.767 | -2.391 | -1.143 | 3.001 | -4.797 | 2.21e-05 | 9.51e-03 | 2.595 | erythrocyte membrane protein 1 (PfEMP1), exon 2 | VAR |
| 156 | PF3D7_0626200 | Pf3D7_06_v3 | 1058666 | - | 1257 | 1.729 | 1.206 | 2.252 | 2.767 | 4.702 | 2.98e-05 | 9.51e-03 | 2.324 | conserved Plasmodium protein, unknown function | NA |
| 238 | PF3D7_0900100 | Pf3D7_09_v3 | 20080 | + | 7806 | -1.469 | -1.999 | -0.940 | 4.728 | -5.062 | 9.47e-06 | 9.51e-03 | 3.443 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 302 | PF3D7_1023600 | Pf3D7_10_v3 | 987358 | - | 2791 | -1.830 | -2.404 | -1.256 | -0.002 | -4.772 | 2.39e-05 | 9.51e-03 | 2.211 | conserved Plasmodium protein, unknown function | NA |
| 340 | PF3D7_1123100 | Pf3D7_11_v3 | 909366 | + | 6959 | -0.572 | -1.113 | -0.031 | 9.128 | -4.775 | 2.37e-05 | 9.51e-03 | 2.476 | calcium-dependent protein kinase 7 | CDPK7 |
| 431 | PF3D7_1255200 | Pf3D7_12_v3 | 2241271 | - | 7692 | -1.472 | -2.856 | -0.088 | 4.501 | -5.017 | 1.09e-05 | 9.51e-03 | 3.308 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 449 | PF3D7_1318300 | Pf3D7_13_v3 | 753910 | + | 5523 | -1.202 | -1.561 | -0.843 | 5.739 | -4.824 | 2.03e-05 | 9.51e-03 | 2.722 | conserved Plasmodium protein, unknown function | NA |
| 561 | PF3D7_1451800 | Pf3D7_14_v3 | 2123461 | + | 3139 | -0.858 | -1.551 | -0.166 | 4.582 | -4.721 | 2.81e-05 | 9.51e-03 | 2.439 | sortilin | NA |
| 8 | PF3D7_0109700 | Pf3D7_01_v3 | 379149 | - | 658 | -1.506 | -2.567 | -0.445 | 4.189 | -4.673 | 3.27e-05 | 9.67e-03 | 2.297 | rRNA biogenesis protein RRP36, putative | RRP36 |
| 179 | PF3D7_0712600 | Pf3D7_07_v3 | 566726 | - | 7583 | -1.776 | -2.493 | -1.059 | 3.427 | -4.632 | 3.78e-05 | 9.79e-03 | 2.147 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 255 | PF3D7_0917800 | Pf3D7_09_v3 | 734629 | + | 1314 | 1.904 | 1.427 | 2.380 | 1.361 | 4.576 | 4.43e-05 | 9.79e-03 | 1.862 | conserved Plasmodium protein, unknown function | NA |
| 379 | PF3D7_1213100 | Pf3D7_12_v3 | 576417 | - | 164 | -2.457 | -2.730 | -2.184 | 2.284 | -4.631 | 3.98e-05 | 9.79e-03 | 2.014 | U1 spliceosomal RNA | NA |
| 390 | PF3D7_1223900 | Pf3D7_12_v3 | 972710 | - | 684 | -2.060 | -2.353 | -1.767 | 2.684 | -4.612 | 4.24e-05 | 9.79e-03 | 2.051 | 50S ribosomal protein L24, putative | NA |
| 447 | PF3D7_1316600 | Pf3D7_13_v3 | 691014 | + | 3112 | -1.238 | -2.069 | -0.406 | 6.487 | -4.584 | 4.49e-05 | 9.79e-03 | 1.953 | choline-phosphate cytidylyltransferase | CCT |
| 321 | PF3D7_1105100 | Pf3D7_11_v3 | 226065 | + | 354 | -0.960 | -1.671 | -0.249 | 9.757 | -4.561 | 4.74e-05 | 9.81e-03 | 1.814 | histone H2B | H2B |
| 78 | PF3D7_0419800 | Pf3D7_04_v3 | 874811 | - | 711 | 0.716 | -1.083 | 2.515 | 5.909 | 4.472 | 6.14e-05 | 1.11e-02 | 1.682 | 60S ribosomal protein L7ae/L30e, putative | NA |
| 110 | PF3D7_0519500 | Pf3D7_05_v3 | 801450 | - | 7678 | -0.939 | -1.829 | -0.050 | 7.051 | -4.496 | 5.70e-05 | 1.11e-02 | 1.702 | carbon catabolite repressor protein 4, putative | CCR4 |
| 232 | PF3D7_0830300 | Pf3D7_08_v3 | 1290240 | - | 1167 | 1.706 | 1.309 | 2.104 | 1.974 | 4.482 | 5.95e-05 | 1.11e-02 | 1.663 | sporozoite invasion-associated protein 2 | SIAP2 |
| 161 | PF3D7_0632800 | Pf3D7_06_v3 | 1374797 | - | 7831 | -1.339 | -1.647 | -1.031 | 4.626 | -4.427 | 7.06e-05 | 1.17e-02 | 1.598 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 205 | PF3D7_0805600 | Pf3D7_08_v3 | 312034 | + | 927 | 0.854 | 0.534 | 1.174 | 7.166 | 4.437 | 6.86e-05 | 1.17e-02 | 1.517 | PAP2-like protein, putative | NA |
| 9 | PF3D7_0113000 | Pf3D7_01_v3 | 487892 | - | 2236 | -1.616 | -2.626 | -0.607 | 11.389 | -4.434 | 8.44e-05 | 1.34e-02 | 1.297 | glutamic acid-rich protein | GARP |
| 398 | PF3D7_1230500 | Pf3D7_12_v3 | 1253973 | - | 1509 | 0.991 | 0.394 | 1.587 | 4.457 | 4.358 | 8.75e-05 | 1.34e-02 | 1.402 | WD repeat-containing protein, putative | NA |
| 307 | PF3D7_1028000 | Pf3D7_10_v3 | 1160031 | + | 3391 | -0.965 | -2.000 | 0.070 | 6.451 | -4.321 | 9.84e-05 | 1.36e-02 | 1.207 | methyltransferase, putative | NA |
| 391 | PF3D7_1224000 | Pf3D7_12_v3 | 974372 | + | 1170 | -1.561 | -1.919 | -1.204 | 2.752 | -4.337 | 9.34e-05 | 1.36e-02 | 1.333 | GTP cyclohydrolase I | GCH1 |
| 423 | PF3D7_1249000 | Pf3D7_12_v3 | 2005175 | - | 2019 | 1.054 | 0.057 | 2.051 | 1.209 | 4.320 | 9.87e-05 | 1.36e-02 | 1.181 | conserved Plasmodium membrane protein, unknown function | NA |
| 365 | PF3D7_1200100 | Pf3D7_12_v3 | 16973 | + | 7525 | -1.587 | -2.095 | -1.079 | 4.080 | -4.313 | 1.03e-04 | 1.38e-02 | 1.258 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 29 | PF3D7_0223500 | Pf3D7_02_v3 | 916352 | - | 7297 | -0.985 | -1.643 | -0.327 | 5.295 | -4.252 | 1.22e-04 | 1.39e-02 | 1.076 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 177 | PF3D7_0711200 | Pf3D7_07_v3 | 495238 | + | 3003 | 1.358 | 0.537 | 2.179 | 2.233 | 4.245 | 1.24e-04 | 1.39e-02 | 1.042 | conserved Plasmodium protein, unknown function | NA |
| 201 | PF3D7_0802000 | Pf3D7_08_v3 | 146089 | + | 4194 | -1.481 | -1.878 | -1.084 | 9.158 | -4.326 | 1.11e-04 | 1.39e-02 | 1.065 | glutamate dehydrogenase, putative | GDH3 |
| 208 | PF3D7_0809100 | Pf3D7_08_v3 | 459312 | + | 7256 | -1.692 | -2.453 | -0.930 | 3.274 | -4.264 | 1.19e-04 | 1.39e-02 | 1.122 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 435 | PF3D7_1303000 | Pf3D7_13_v3 | 158144 | + | 635 | -1.142 | -2.019 | -0.265 | 3.361 | -4.271 | 1.15e-04 | 1.39e-02 | 1.162 | conserved Plasmodium protein, unknown function | NA |
| 467 | PF3D7_1344800 | Pf3D7_13_v3 | 1796274 | + | 1436 | -0.754 | -1.088 | -0.420 | 6.277 | -4.260 | 1.19e-04 | 1.39e-02 | 1.045 | aspartate carbamoyltransferase | ATCase |
| 357 | PF3D7_1140200 | Pf3D7_11_v3 | 1601257 | - | 1822 | -1.598 | -2.428 | -0.767 | 3.868 | -4.232 | 1.33e-04 | 1.45e-02 | 1.028 | conserved Plasmodium protein, unknown function | NA |
| 6 | PF3D7_0106000 | Pf3D7_01_v3 | 255775 | - | 2769 | 1.082 | -0.403 | 2.567 | 1.575 | 4.186 | 1.49e-04 | 1.55e-02 | 0.855 | conserved Plasmodium protein, unknown function | NA |
| 549 | PF3D7_1445600 | Pf3D7_14_v3 | 1871778 | + | 2604 | 0.758 | -0.019 | 1.536 | 8.240 | 4.184 | 1.50e-04 | 1.55e-02 | 0.739 | RNA-binding protein, putative | NA |
| 163 | PF3D7_0703100 | Pf3D7_07_v3 | 121414 | + | 543 | 0.953 | 0.263 | 1.643 | 3.538 | 4.162 | 1.60e-04 | 1.61e-02 | 0.861 | conserved Plasmodium protein, unknown function | NA |
| 565 | PF3D7_1457000 | Pf3D7_14_v3 | 2336649 | - | 2505 | -0.729 | -1.154 | -0.304 | 8.941 | -4.157 | 1.63e-04 | 1.61e-02 | 0.648 | signal peptide peptidase | SPP |
| 131 | PF3D7_0532300 | Pf3D7_05_v3 | 1308278 | + | 1663 | -1.393 | -1.808 | -0.978 | 10.836 | -4.180 | 1.74e-04 | 1.68e-02 | 0.615 | Plasmodium exported protein (PHISTb), unknown function | NA |
| 32 | PF3D7_0302800 | Pf3D7_03_v3 | 148046 | - | 1260 | 1.219 | 0.925 | 1.512 | 5.255 | 4.099 | 1.98e-04 | 1.82e-02 | 0.629 | conserved Plasmodium protein, unknown function | NA |
| 353 | PF3D7_1135300 | Pf3D7_11_v3 | 1381015 | - | 1230 | 1.241 | 0.106 | 2.377 | 2.278 | 4.080 | 2.06e-04 | 1.82e-02 | 0.611 | conserved Plasmodium membrane protein, unknown function | NA |
| 372 | PF3D7_1206300 | Pf3D7_12_v3 | 281020 | - | 8283 | -1.582 | -2.221 | -0.943 | 1.502 | -4.094 | 1.97e-04 | 1.82e-02 | 0.619 | conserved Plasmodium protein, unknown function | NA |
| 412 | PF3D7_1244200 | Pf3D7_12_v3 | 1852844 | - | 2838 | 1.134 | 0.645 | 1.623 | 5.492 | 4.087 | 2.03e-04 | 1.82e-02 | 0.589 | RNA polymerase II transcription factor B subunit 2, putative | TFB2 |
| 129 | PF3D7_0529000 | Pf3D7_05_v3 | 1186787 | - | 2160 | 0.475 | -0.143 | 1.092 | 7.634 | 4.064 | 2.17e-04 | 1.84e-02 | 0.409 | conserved Plasmodium protein, unknown function | NA |
| 222 | PF3D7_0822200 | Pf3D7_08_v3 | 982570 | + | 5127 | 1.148 | 0.789 | 1.508 | 2.978 | 4.038 | 2.34e-04 | 1.84e-02 | 0.519 | conserved Plasmodium membrane protein, unknown function | NA |
| 262 | PF3D7_0925300 | Pf3D7_09_v3 | 1019164 | - | 1740 | 1.901 | 1.624 | 2.177 | 0.157 | 4.031 | 2.39e-04 | 1.84e-02 | 0.362 | proline–tRNA ligase, putative | aPRS |
| 332 | PF3D7_1118400 | Pf3D7_11_v3 | 699869 | - | 921 | 1.121 | 0.356 | 1.885 | 3.285 | 4.055 | 2.22e-04 | 1.84e-02 | 0.568 | haloacid dehalogenase-like hydrolase, putative | NA |
| 396 | PF3D7_1228800 | Pf3D7_12_v3 | 1169557 | - | 9630 | -0.548 | -0.835 | -0.262 | 6.866 | -4.059 | 2.19e-04 | 1.84e-02 | 0.432 | WD repeat-containing protein, putative | NA |
| 480 | PF3D7_1354300 | Pf3D7_13_v3 | 2164239 | - | 3178 | -0.548 | -1.100 | 0.004 | 9.446 | -4.036 | 2.36e-04 | 1.84e-02 | 0.284 | large subunit rRNA methyltransferase, putative | NA |
| 580 | PF3D7_1470200 | Pf3D7_14_v3 | 2877586 | - | 1163 | -0.728 | -1.031 | -0.425 | 5.419 | -4.044 | 2.30e-04 | 1.84e-02 | 0.484 | conserved Plasmodium protein, unknown function | NA |
| 1 | mal_rna_11:rRNA | M76611 | 1916 | - | 108 | -1.715 | -2.483 | -0.948 | 1.846 | -3.991 | 2.70e-04 | 1.84e-02 | 0.352 | NA | NA |
| 14 | PF3D7_0201900 | Pf3D7_02_v3 | 91318 | - | 7521 | -1.731 | -2.587 | -0.876 | 10.606 | -4.025 | 2.92e-04 | 1.84e-02 | 0.144 | erythrocyte membrane protein 3 | EMP3 |
| 28 | PF3D7_0220500 | Pf3D7_02_v3 | 823825 | - | 1040 | -1.038 | -1.822 | -0.255 | 6.499 | -3.965 | 2.97e-04 | 1.84e-02 | 0.181 | Plasmodium exported protein (hyp2), unknown function | NA |
| 151 | PF3D7_0622700 | Pf3D7_06_v3 | 916000 | - | 1300 | 1.664 | 0.942 | 2.387 | 1.445 | 3.971 | 2.87e-04 | 1.84e-02 | 0.296 | conserved Plasmodium membrane protein, unknown function | NA |
| 198 | PF3D7_0800100 | Pf3D7_08_v3 | 21361 | + | 7293 | -1.635 | -2.151 | -1.119 | 4.419 | -3.980 | 2.94e-04 | 1.84e-02 | 0.310 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 378 | PF3D7_1212800 | Pf3D7_12_v3 | 565966 | + | 966 | 1.057 | 0.718 | 1.397 | 2.461 | 3.989 | 2.71e-04 | 1.84e-02 | 0.377 | iron-sulfur subunit of succinate dehydrogenase | NA |
| 393 | PF3D7_1225600 | Pf3D7_12_v3 | 1035261 | - | 2895 | -0.530 | -1.045 | -0.015 | 8.015 | -4.000 | 2.63e-04 | 1.84e-02 | 0.210 | conserved Plasmodium protein, unknown function | NA |
| 417 | PF3D7_1246600 | Pf3D7_12_v3 | 1936522 | + | 1173 | -0.817 | -1.610 | -0.024 | 5.429 | -3.970 | 2.87e-04 | 1.84e-02 | 0.271 | pre-mRNA-splicing factor CWC26, putative | BUD13 |
| 438 | PF3D7_1305400 | Pf3D7_13_v3 | 268785 | - | 1953 | 0.657 | -0.823 | 2.136 | 5.323 | 4.013 | 2.53e-04 | 1.84e-02 | 0.394 | AAR2 protein, putative | NA |
| 441 | PF3D7_1307700 | Pf3D7_13_v3 | 344525 | + | 3708 | 0.667 | -0.041 | 1.375 | 6.400 | 4.021 | 2.47e-04 | 1.84e-02 | 0.350 | conserved Plasmodium protein, unknown function | NA |
| 517 | PF3D7_1414200 | Pf3D7_14_v3 | 564024 | - | 1224 | 0.759 | -0.314 | 1.832 | 5.905 | 3.959 | 2.97e-04 | 1.84e-02 | 0.212 | conserved Plasmodium protein, unknown function | NA |
| 525 | PF3D7_1421150 | Pf3D7_14_v3 | 875173 | - | 149 | -1.635 | -2.311 | -0.959 | 1.041 | -3.963 | 2.93e-04 | 1.84e-02 | 0.237 | C/D small nucleolar RNA | NA |
| 547 | PF3D7_1444800 | Pf3D7_14_v3 | 1844041 | - | 1577 | -0.762 | -1.476 | -0.048 | 10.314 | -3.999 | 2.63e-04 | 1.84e-02 | 0.184 | fructose-bisphosphate aldolase | FBPA |
| 60 | PF3D7_0404600 | Pf3D7_04_v3 | 247731 | + | 12417 | -1.517 | -1.762 | -1.272 | 7.591 | -3.910 | 3.91e-04 | 2.00e-02 | -0.094 | conserved Plasmodium membrane protein, unknown function | NA |
| 62 | PF3D7_0404900 | Pf3D7_04_v3 | 267244 | - | 1137 | 1.762 | 1.387 | 2.137 | 3.392 | 3.926 | 3.41e-04 | 2.00e-02 | 0.192 | 6-cysteine protein | P41 |
| 68 | PF3D7_0412700 | Pf3D7_04_v3 | 561667 | - | 7676 | -1.390 | -2.006 | -0.774 | 4.815 | -3.878 | 3.92e-04 | 2.00e-02 | 0.031 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 166 | PF3D7_0704600 | Pf3D7_07_v3 | 216024 | - | 13049 | -0.601 | -0.849 | -0.353 | 10.219 | -3.887 | 3.68e-04 | 2.00e-02 | -0.143 | E3 ubiquitin-protein ligase | UT |
| 182 | PF3D7_0713600 | Pf3D7_07_v3 | 617933 | + | 2935 | 1.307 | 0.675 | 1.939 | 3.292 | 3.912 | 3.42e-04 | 2.00e-02 | 0.186 | mitochondrial ribosomal protein S5 precursor, putative | NA |
| 204 | PF3D7_0804900 | Pf3D7_08_v3 | 279711 | - | 1476 | 0.931 | 0.413 | 1.449 | 5.943 | 3.898 | 3.57e-04 | 2.00e-02 | 0.039 | GTPase-activating protein, putative | NA |
| 225 | PF3D7_0823200 | Pf3D7_08_v3 | 1022629 | - | 1218 | -0.667 | -1.309 | -0.024 | 9.598 | -3.887 | 3.69e-04 | 2.00e-02 | -0.141 | RNA-binding protein, putative | NA |
| 273 | PF3D7_1000100 | Pf3D7_10_v3 | 28490 | + | 7675 | -1.293 | -1.978 | -0.608 | 4.472 | -3.882 | 3.79e-04 | 2.00e-02 | 0.072 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 314 | PF3D7_1100100 | Pf3D7_11_v3 | 24160 | + | 7439 | -1.070 | -1.527 | -0.612 | 4.769 | -3.921 | 3.33e-04 | 2.00e-02 | 0.174 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 326 | PF3D7_1108700 | Pf3D7_11_v3 | 373238 | - | 1623 | 0.790 | 0.254 | 1.326 | 6.852 | 3.899 | 3.55e-04 | 2.00e-02 | -0.012 | heat shock protein DnaJ homologue Pfj2 | NA |
| 331 | PF3D7_1115200 | Pf3D7_11_v3 | 576773 | + | 3504 | -0.688 | -1.153 | -0.222 | 8.257 | -3.873 | 3.84e-04 | 2.00e-02 | -0.152 | histone-lysine N-methyltransferase SET7 | SET7 |
| 336 | PF3D7_1121100 | Pf3D7_11_v3 | 794254 | - | 5308 | -0.787 | -1.146 | -0.428 | 8.462 | -3.879 | 3.78e-04 | 2.00e-02 | -0.128 | conserved Plasmodium protein, unknown function | NA |
| 448 | PF3D7_1316900 | Pf3D7_13_v3 | 701047 | - | 2877 | 0.669 | 0.447 | 0.890 | 7.724 | 3.893 | 3.62e-04 | 2.00e-02 | -0.078 | conserved Plasmodium protein, unknown function | NA |
| 470 | PF3D7_1346200 | Pf3D7_13_v3 | 1845878 | - | 507 | 2.097 | 1.692 | 2.503 | 0.972 | 3.900 | 3.62e-04 | 2.00e-02 | 0.074 | nuclear import protein MOG1, putative | NA |
| 84 | PF3D7_0500100 | Pf3D7_05_v3 | 20929 | + | 7528 | -1.296 | -1.730 | -0.862 | 3.384 | -3.852 | 4.10e-04 | 2.01e-02 | 0.026 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 147 | PF3D7_0617200 | Pf3D7_06_v3 | 717050 | + | 1868 | -1.075 | -1.588 | -0.563 | 7.942 | -3.873 | 4.08e-04 | 2.01e-02 | -0.187 | conserved Plasmodium protein, unknown function | NA |
| 226 | PF3D7_0823800 | Pf3D7_08_v3 | 1043813 | + | 1968 | -0.846 | -1.237 | -0.454 | 5.211 | -3.848 | 4.14e-04 | 2.01e-02 | -0.075 | DnaJ protein, putative | NA |
| 343 | PF3D7_1126300 | Pf3D7_11_v3 | 1026976 | + | 2569 | 1.116 | 0.621 | 1.612 | 4.598 | 3.845 | 4.18e-04 | 2.01e-02 | -0.032 | DnaJ protein, putative | NA |
| 394 | PF3D7_1226600 | Pf3D7_12_v3 | 1077868 | - | 909 | 1.632 | 0.899 | 2.365 | -0.314 | 3.852 | 4.09e-04 | 2.01e-02 | -0.109 | proliferating cell nuclear antigen 2 | PCNA2 |
| 389 | PF3D7_1223400 | Pf3D7_12_v3 | 941125 | + | 5621 | -0.716 | -1.080 | -0.353 | 11.240 | -3.839 | 4.26e-04 | 2.03e-02 | -0.277 | phospholipid-transporting ATPase, putative | NA |
| 173 | PF3D7_0708500 | Pf3D7_07_v3 | 385583 | - | 2739 | -0.777 | -1.070 | -0.484 | 6.710 | -3.831 | 4.35e-04 | 2.03e-02 | -0.202 | heat shock protein 86 family protein | NA |
| 492 | PF3D7_1365600 | Pf3D7_13_v3 | 2621261 | + | 2740 | 0.751 | 0.214 | 1.288 | 4.165 | 3.835 | 4.31e-04 | 2.03e-02 | -0.034 | DNA topoisomerase VI, b subunit, putative | NA |
| 13 | PF3D7_0201800 | Pf3D7_02_v3 | 86832 | - | 1960 | -0.631 | -1.267 | 0.004 | 9.431 | -3.809 | 4.65e-04 | 2.05e-02 | -0.356 | knob associated heat shock protein 40 | KAHsp40 |
| 98 | PF3D7_0512000 | Pf3D7_05_v3 | 527639 | + | 1028 | -1.003 | -1.949 | -0.057 | 5.293 | -3.812 | 4.61e-04 | 2.05e-02 | -0.163 | prefoldin subunit 6, putative | NA |
| 277 | PF3D7_1003900 | Pf3D7_10_v3 | 177921 | + | 950 | 1.720 | 0.913 | 2.527 | 0.292 | 3.815 | 4.58e-04 | 2.05e-02 | -0.161 | conserved Plasmodium protein, unknown function | NA |
| 281 | PF3D7_1009300 | Pf3D7_10_v3 | 377906 | - | 1803 | 1.321 | 0.834 | 1.808 | 3.025 | 3.811 | 4.63e-04 | 2.05e-02 | -0.082 | conserved Plasmodium protein, unknown function | NA |
| 291 | PF3D7_1016100 | Pf3D7_10_v3 | 643558 | - | 774 | 1.267 | 0.935 | 1.599 | 0.676 | 3.817 | 4.55e-04 | 2.05e-02 | -0.137 | conserved Plasmodium protein, unknown function | NA |
| 93 | PF3D7_0509000 | Pf3D7_05_v3 | 376855 | - | 1598 | -0.556 | -2.114 | 1.002 | 5.821 | -3.788 | 4.96e-04 | 2.14e-02 | -0.267 | SNAP protein (soluble N-ethylmaleimide-sensitive factor attachment protein), putative | NA |
| 432 | PF3D7_1301400 | Pf3D7_13_v3 | 82718 | + | 1301 | -1.218 | -2.217 | -0.219 | 8.056 | -3.813 | 4.95e-04 | 2.14e-02 | -0.337 | Plasmodium exported protein (hyp12), unknown function | HYP12 |
| 22 | PF3D7_0209700 | Pf3D7_02_v3 | 400153 | - | 1707 | 0.605 | -0.707 | 1.917 | 8.782 | 3.780 | 5.07e-04 | 2.17e-02 | -0.427 | RING zinc finger protein, putative | NA |
| 45 | PF3D7_0317500 | Pf3D7_03_v3 | 716523 | - | 5309 | 0.696 | 0.032 | 1.361 | 7.107 | 3.771 | 5.20e-04 | 2.19e-02 | -0.390 | kinesin-5 | EG5 |
| 220 | PF3D7_0821500 | Pf3D7_08_v3 | 967901 | - | 840 | 0.850 | 0.612 | 1.088 | 4.882 | 3.763 | 5.33e-04 | 2.19e-02 | -0.262 | ribosomal RNA small subunit methyltransferase NEP1, putative | NEP1 |
| 333 | PF3D7_1119200 | Pf3D7_11_v3 | 722717 | - | 573 | -1.138 | -2.235 | -0.040 | 3.872 | -3.769 | 5.24e-04 | 2.19e-02 | -0.200 | conserved protein, unknown function | NA |
| 482 | PF3D7_1355700 | Pf3D7_13_v3 | 2206592 | - | 3867 | 1.310 | 0.512 | 2.109 | 7.281 | 3.793 | 5.34e-04 | 2.19e-02 | -0.399 | NLI interacting factor-like phosphatase, putative | NIF3 |
| 500 | PF3D7_1401400 | Pf3D7_14_v3 | 53411 | - | 324 | -0.820 | -1.224 | -0.416 | 12.486 | -3.765 | 5.38e-04 | 2.19e-02 | -0.485 | early transcribed membrane protein 14.1 | ETRAMP14 |
| 130 | PF3D7_0531000 | Pf3D7_05_v3 | 1267410 | + | 2130 | 0.770 | 0.513 | 1.027 | 5.006 | 3.744 | 5.64e-04 | 2.27e-02 | -0.321 | conserved Plasmodium protein, unknown function | NA |
| 341 | PF3D7_1124800 | Pf3D7_11_v3 | 976880 | - | 1057 | -0.601 | -0.891 | -0.311 | 6.706 | -3.738 | 5.74e-04 | 2.29e-02 | -0.458 | nuclear preribosomal assembly protein, putative | NA |
| 77 | PF3D7_0419500 | Pf3D7_04_v3 | 866501 | - | 1611 | 1.278 | -0.047 | 2.603 | 3.860 | 3.728 | 5.91e-04 | 2.29e-02 | -0.312 | conserved Plasmodium membrane protein, unknown function | NA |
| 187 | PF3D7_0717600 | Pf3D7_07_v3 | 758720 | - | 4158 | -1.552 | -1.881 | -1.222 | 3.062 | -3.737 | 5.89e-04 | 2.29e-02 | -0.295 | conserved Plasmodium protein, unknown function | NA |
| 272 | PF3D7_0936800 | Pf3D7_09_v3 | 1458392 | + | 1471 | -1.129 | -1.403 | -0.854 | 10.817 | -3.758 | 5.84e-04 | 2.29e-02 | -0.546 | Plasmodium exported protein (PHISTc), unknown function | NA |
| 92 | PF3D7_0508700 | Pf3D7_05_v3 | 358261 | + | 4473 | -0.502 | -1.380 | 0.376 | 7.632 | -3.707 | 6.29e-04 | 2.34e-02 | -0.595 | pre-mRNA-processing ATP-dependent RNA helicase PRP5, putative | PRP5 |
| 159 | PF3D7_0629600 | Pf3D7_06_v3 | 1218307 | + | 945 | 0.513 | 0.284 | 0.742 | 4.955 | 3.711 | 6.21e-04 | 2.34e-02 | -0.409 | conserved Plasmodium protein, unknown function | NA |
| 297 | PF3D7_1019100 | Pf3D7_10_v3 | 766168 | - | 5787 | -1.541 | -1.883 | -1.198 | 0.833 | -3.705 | 6.33e-04 | 2.34e-02 | -0.392 | conserved Plasmodium protein, unknown function | NA |
| 317 | PF3D7_1102800 | Pf3D7_11_v3 | 131703 | - | 285 | -0.917 | -1.176 | -0.657 | 13.477 | -3.727 | 6.12e-04 | 2.34e-02 | -0.593 | early transcribed membrane protein 11.2 | ETRAMP11.2 |
| 361 | PF3D7_1145500 | Pf3D7_11_v3 | 1807359 | + | 2772 | 1.127 | 0.388 | 1.866 | 1.570 | 3.708 | 6.28e-04 | 2.34e-02 | -0.364 | ABC transporter B family member 3, putative | ABCB3 |
| 240 | PF3D7_0903200 | Pf3D7_09_v3 | 133762 | - | 1826 | -0.871 | -1.268 | -0.475 | 5.122 | -3.701 | 6.40e-04 | 2.35e-02 | -0.460 | ras-related protein RAB7 | RAB7 |
| 264 | PF3D7_0928500 | Pf3D7_09_v3 | 1146239 | - | 959 | -1.140 | -2.966 | 0.686 | 2.706 | -3.698 | 6.46e-04 | 2.35e-02 | -0.375 | conserved Plasmodium protein, unknown function | NA |
| 408 | PF3D7_1240900 | Pf3D7_12_v3 | 1735543 | + | 7866 | -1.353 | -1.614 | -1.092 | 4.223 | -3.693 | 6.65e-04 | 2.40e-02 | -0.422 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 137 | PF3D7_0606800 | Pf3D7_06_v3 | 288377 | - | 900 | 1.561 | 0.769 | 2.354 | 3.353 | 3.686 | 6.84e-04 | 2.40e-02 | -0.426 | probable protein, unknown function | NA |
| 466 | PF3D7_1344200 | Pf3D7_13_v3 | 1769129 | + | 2799 | -0.566 | -1.078 | -0.055 | 9.450 | -3.679 | 6.83e-04 | 2.40e-02 | -0.720 | heat shock protein 110, putative | HSP110 |
| 552 | PF3D7_1446900 | Pf3D7_14_v3 | 1924425 | - | 2226 | 0.742 | 0.467 | 1.017 | 6.855 | 3.679 | 6.83e-04 | 2.40e-02 | -0.624 | glutaminyl-peptide cyclotransferase, putative | NA |
| 235 | PF3D7_0831700 | Pf3D7_08_v3 | 1365467 | - | 2040 | -0.882 | -1.398 | -0.366 | 13.476 | -3.683 | 6.92e-04 | 2.41e-02 | -0.708 | heat shock protein 70 | HSP70-x |
| 165 | PF3D7_0703400 | Pf3D7_07_v3 | 129370 | - | 2463 | 1.213 | 0.733 | 1.693 | 3.356 | 3.663 | 7.15e-04 | 2.47e-02 | -0.470 | conserved Plasmodium protein, unknown function | NA |
| 582 | PF3D7_1472300 | Pf3D7_14_v3 | 2954108 | + | 3001 | 1.117 | 0.747 | 1.486 | 4.456 | 3.650 | 7.44e-04 | 2.55e-02 | -0.544 | conserved Plasmodium membrane protein, unknown function | NA |
| 180 | PF3D7_0712800 | Pf3D7_07_v3 | 581386 | - | 7538 | -1.220 | -1.762 | -0.678 | 4.050 | -3.644 | 7.56e-04 | 2.55e-02 | -0.534 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 322 | PF3D7_1105300 | Pf3D7_11_v3 | 231847 | - | 2392 | 1.349 | 0.827 | 1.871 | 1.730 | 3.646 | 7.51e-04 | 2.55e-02 | -0.515 | conserved Plasmodium protein, unknown function | NA |
| 533 | PF3D7_1428100 | Pf3D7_14_v3 | 1098038 | - | 1914 | 0.940 | 0.663 | 1.217 | 3.882 | 3.633 | 7.82e-04 | 2.61e-02 | -0.565 | WW domain-binding protein 11, putative | NA |
| 292 | PF3D7_1016200 | Pf3D7_10_v3 | 646054 | + | 1683 | 1.116 | 0.713 | 1.519 | 4.605 | 3.619 | 8.13e-04 | 2.70e-02 | -0.636 | Rab3 GTPase-activating protein non-catalytic subunit, putative | NA |
| 63 | PF3D7_0405400 | Pf3D7_04_v3 | 291251 | + | 9726 | -0.560 | -1.202 | 0.081 | 10.721 | -3.607 | 8.43e-04 | 2.71e-02 | -0.921 | pre-mRNA-processing-splicing factor 8, putative | PRPF8 |
| 194 | PF3D7_0723900 | Pf3D7_07_v3 | 1000701 | - | 4046 | -0.617 | -1.753 | 0.519 | 7.841 | -3.606 | 8.45e-04 | 2.71e-02 | -0.878 | RNA-binding protein, putative | NA |
| 445 | PF3D7_1309600 | Pf3D7_13_v3 | 438510 | + | 867 | 0.851 | 0.427 | 1.276 | 4.331 | 3.613 | 8.28e-04 | 2.71e-02 | -0.632 | ribosomal RNA methyltransferase, putative | NA |
| 452 | PF3D7_1321700 | Pf3D7_13_v3 | 902383 | + | 2784 | -0.549 | -1.144 | 0.046 | 9.143 | -3.606 | 8.44e-04 | 2.71e-02 | -0.915 | splicing factor 1 | SF1 |
| 303 | PF3D7_1025000 | Pf3D7_10_v3 | 1045608 | - | 4153 | -0.567 | -1.130 | -0.005 | 8.288 | -3.596 | 8.69e-04 | 2.75e-02 | -0.912 | formin 2, putative | NA |
| 512 | PF3D7_1410500 | Pf3D7_14_v3 | 423751 | - | 500 | 1.138 | 0.408 | 1.869 | 1.432 | 3.596 | 8.71e-04 | 2.75e-02 | -0.649 | conserved Plasmodium protein, unknown function | NA |
| 489 | PF3D7_1364000 | Pf3D7_13_v3 | 2564625 | + | 2484 | 1.063 | 0.739 | 1.388 | 3.834 | 3.586 | 8.95e-04 | 2.81e-02 | -0.680 | conserved Plasmodium protein, unknown function | NA |
| 443 | PF3D7_1309100 | Pf3D7_13_v3 | 418820 | + | 1302 | -0.800 | -1.672 | 0.073 | 8.874 | -3.580 | 9.25e-04 | 2.88e-02 | -0.995 | 60S ribosomal protein L24, putative | NA |
| 100 | PF3D7_0513600 | Pf3D7_05_v3 | 574941 | - | 3565 | -0.958 | -2.280 | 0.365 | 5.653 | -3.563 | 9.64e-04 | 2.96e-02 | -0.872 | deoxyribodipyrimidine photo-lyase, putative | NA |
| 433 | PF3D7_1302700 | Pf3D7_13_v3 | 145174 | + | 5025 | -0.478 | -1.596 | 0.641 | 8.872 | -3.562 | 9.60e-04 | 2.96e-02 | -1.031 | ATP-dependent RNA helicase DHR1, putative | NA |
| 382 | PF3D7_1215900 | Pf3D7_12_v3 | 641552 | + | 1968 | 0.843 | 0.572 | 1.113 | 4.860 | 3.553 | 9.86e-04 | 3.00e-02 | -0.822 | serpentine receptor, putative | SR10 |
| 12 | PF3D7_0201600 | Pf3D7_02_v3 | 77251 | - | 1558 | -0.800 | -1.061 | -0.538 | 9.183 | -3.546 | 1.02e-03 | 3.01e-02 | -1.077 | PHISTb domain-containing RESA-like protein 1 | RLP1 |
| 25 | PF3D7_0218700 | Pf3D7_02_v3 | 763491 | - | 1701 | -0.710 | -1.254 | -0.167 | 7.132 | -3.547 | 1.00e-03 | 3.01e-02 | -1.000 | pre-mRNA-processing protein 45, putative | PRP45 |
| 72 | PF3D7_0416100 | Pf3D7_04_v3 | 706529 | + | 2481 | -1.006 | -1.674 | -0.337 | 4.181 | -3.533 | 1.05e-03 | 3.01e-02 | -0.855 | glutamyl-tRNA(Gln) amidotransferase subunit A | GATA |
| 150 | PF3D7_0621500 | Pf3D7_06_v3 | 881963 | + | 1032 | 1.105 | 0.673 | 1.537 | 1.210 | 3.537 | 1.03e-03 | 3.01e-02 | -0.795 | ribonuclease P/MRP protein subunit RPP1, putative | RPP1 |
| 374 | PF3D7_1208600 | Pf3D7_12_v3 | 402300 | + | 228 | -0.766 | -1.004 | -0.528 | 3.774 | -3.537 | 1.03e-03 | 3.01e-02 | -0.819 | mitochondrial import inner membrane translocase subunit TIM10, putative | TIM10 |
| 541 | PF3D7_1437800 | Pf3D7_14_v3 | 1530276 | - | 555 | 1.908 | 1.376 | 2.440 | 2.848 | 3.556 | 1.02e-03 | 3.01e-02 | -0.767 | trafficking protein particle complex subunit 5, putative | TRAPPC5 |
| 555 | PF3D7_1449900 | Pf3D7_14_v3 | 2044007 | - | 1023 | 1.254 | 0.706 | 1.803 | 2.664 | 3.544 | 1.01e-03 | 3.01e-02 | -0.765 | conserved Plasmodium protein, unknown function | NA |
| 567 | PF3D7_1457900 | Pf3D7_14_v3 | 2375579 | + | 10368 | -0.647 | -0.867 | -0.426 | 5.665 | -3.533 | 1.04e-03 | 3.01e-02 | -0.933 | conserved Plasmodium protein, unknown function | NA |
| 413 | PF3D7_1244300 | Pf3D7_12_v3 | 1857849 | + | 242 | -1.943 | -2.298 | -1.587 | 2.556 | -3.524 | 1.11e-03 | 3.18e-02 | -0.840 | ACEA small nucleolar RNA U3 | NA |
| 279 | PF3D7_1004400 | Pf3D7_10_v3 | 207000 | - | 2643 | -0.851 | -1.643 | -0.059 | 5.835 | -3.497 | 1.16e-03 | 3.26e-02 | -1.046 | RNA-binding protein, putative | NA |
| 550 | PF3D7_1445800 | Pf3D7_14_v3 | 1878658 | - | 3920 | 1.031 | 0.476 | 1.587 | 1.557 | 3.498 | 1.16e-03 | 3.26e-02 | -0.883 | conserved Plasmodium membrane protein, unknown function | NA |
| 568 | PF3D7_1458000 | Pf3D7_14_v3 | 2387786 | + | 1710 | 0.358 | -0.401 | 1.117 | 8.181 | 3.495 | 1.16e-03 | 3.26e-02 | -1.188 | cysteine proteinase falcipain 1 | FP1 |
| 213 | PF3D7_0814100 | Pf3D7_08_v3 | 682518 | - | 1055 | 0.932 | 0.352 | 1.512 | 4.301 | 3.479 | 1.22e-03 | 3.31e-02 | -0.979 | conserved Plasmodium protein, unknown function | NA |
| 285 | PF3D7_1013000 | Pf3D7_10_v3 | 500210 | + | 2012 | 1.069 | 0.789 | 1.349 | 2.762 | 3.484 | 1.20e-03 | 3.31e-02 | -0.917 | zinc finger protein, putative | NA |
| 289 | PF3D7_1015600 | Pf3D7_10_v3 | 627044 | - | 1997 | -0.862 | -1.191 | -0.533 | 5.366 | -3.477 | 1.23e-03 | 3.31e-02 | -1.075 | heat shock protein 60 | HSP60 |
| 329 | PF3D7_1111300 | Pf3D7_11_v3 | 442959 | - | 870 | 0.861 | 0.490 | 1.232 | 2.957 | 3.479 | 1.22e-03 | 3.31e-02 | -0.928 | SNARE protein, putative | GS27 |
| 370 | PF3D7_1205700 | Pf3D7_12_v3 | 253155 | + | 969 | 1.137 | 0.380 | 1.894 | 0.854 | 3.476 | 1.23e-03 | 3.31e-02 | -0.947 | targeted glyoxalase II | tGloII |
| 469 | PF3D7_1345200 | Pf3D7_13_v3 | 1812220 | - | 1710 | 0.993 | -0.133 | 2.120 | 3.418 | 3.476 | 1.23e-03 | 3.31e-02 | -0.948 | rhomboid protease ROM6, putative | ROM6 |
| 310 | PF3D7_1035800 | Pf3D7_10_v3 | 1420533 | + | 2139 | -1.550 | -2.352 | -0.748 | 9.464 | -3.508 | 1.26e-03 | 3.32e-02 | -1.229 | probable protein, unknown function | M712 |
| 359 | PF3D7_1142400 | Pf3D7_11_v3 | 1702089 | - | 1554 | 0.671 | 0.139 | 1.202 | 5.990 | 3.467 | 1.26e-03 | 3.32e-02 | -1.139 | coproporphyrinogen-III oxidase | CPO |
| 403 | PF3D7_1234500 | Pf3D7_12_v3 | 1439896 | - | 1155 | 0.621 | 0.015 | 1.226 | 4.896 | 3.470 | 1.25e-03 | 3.32e-02 | -1.040 | conserved Plasmodium protein, unknown function | NA |
| 455 | PF3D7_1326700 | Pf3D7_13_v3 | 1125280 | + | 1629 | 1.449 | 0.663 | 2.236 | 3.645 | 3.474 | 1.26e-03 | 3.32e-02 | -0.978 | conserved Apicomplexan protein, unknown function | NA |
| 299 | PF3D7_1021900 | Pf3D7_10_v3 | 905473 | - | 6873 | -0.918 | -1.171 | -0.664 | 6.810 | -3.462 | 1.31e-03 | 3.37e-02 | -1.223 | PHAX domain-containing protein, putative | NA |
| 454 | PF3D7_1324200 | Pf3D7_13_v3 | 1000100 | - | 1783 | -0.817 | -1.572 | -0.061 | 7.184 | -3.458 | 1.31e-03 | 3.37e-02 | -1.246 | micro-fibrillar-associated protein, putative | NA |
| 518 | PF3D7_1414500 | Pf3D7_14_v3 | 578369 | - | 9161 | -0.606 | -1.509 | 0.297 | 8.009 | -3.454 | 1.31e-03 | 3.37e-02 | -1.297 | atypical protein kinase, ABC-1 family, putative | ABCk2 |
| 90 | PF3D7_0506700 | Pf3D7_05_v3 | 280886 | + | 2460 | -0.677 | -1.739 | 0.385 | 4.990 | -3.449 | 1.33e-03 | 3.38e-02 | -1.122 | GTPase-activating protein, putative | NA |
| 347 | PF3D7_1128100 | Pf3D7_11_v3 | 1094909 | - | 1023 | -0.696 | -1.413 | 0.022 | 5.320 | -3.450 | 1.32e-03 | 3.38e-02 | -1.126 | prefoldin subunit 5, putative | NA |
| 79 | PF3D7_0420000 | Pf3D7_04_v3 | 894612 | - | 10113 | -0.538 | -1.185 | 0.108 | 9.307 | -3.442 | 1.36e-03 | 3.41e-02 | -1.358 | zinc finger protein, putative | NA |
| 114 | PF3D7_0522300 | Pf3D7_05_v3 | 902613 | - | 2232 | -0.540 | -1.220 | 0.140 | 6.719 | -3.442 | 1.36e-03 | 3.41e-02 | -1.260 | S-adenosylmethionine-dependent methyltransferase, putative | NA |
| 442 | PF3D7_1308300 | Pf3D7_13_v3 | 372260 | + | 387 | 0.483 | -0.022 | 0.988 | 7.931 | 3.438 | 1.37e-03 | 3.42e-02 | -1.336 | 40S ribosomal protein S27 | RPS27 |
| 96 | PF3D7_0511000 | Pf3D7_05_v3 | 467585 | - | 516 | -0.570 | -1.189 | 0.049 | 8.143 | -3.432 | 1.39e-03 | 3.46e-02 | -1.350 | translationally-controlled tumor protein homolog | TCTP |
| 89 | PF3D7_0503100 | Pf3D7_05_v3 | 127064 | - | 1614 | -1.195 | -1.694 | -0.696 | 2.285 | -3.424 | 1.43e-03 | 3.47e-02 | -1.059 | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative | IspE |
| 160 | PF3D7_0631600 | Pf3D7_06_v3 | 1323294 | + | 1142 | -1.495 | -2.245 | -0.745 | 2.400 | -3.430 | 1.41e-03 | 3.47e-02 | -1.046 | exported protein family 4 | EPF4 |
| 319 | PF3D7_1103400 | Pf3D7_11_v3 | 146427 | + | 4389 | 1.195 | 0.875 | 1.515 | 3.144 | 3.423 | 1.43e-03 | 3.47e-02 | -1.072 | FeS cluster assembly protein SufD, putative | SufD |
| 364 | PF3D7_1149500 | Pf3D7_11_v3 | 1991359 | - | 2660 | -0.643 | -1.282 | -0.003 | 8.035 | -3.424 | 1.43e-03 | 3.47e-02 | -1.355 | ring-infected erythrocyte surface antigen 2, pseudogene | RESA2 |
| 247 | PF3D7_0907900 | Pf3D7_09_v3 | 367865 | - | 925 | -1.510 | -2.913 | -0.107 | 3.713 | -3.434 | 1.44e-03 | 3.47e-02 | -1.102 | peptide deformylase | |
| 122 | PF3D7_0524800 | Pf3D7_05_v3 | 1021408 | - | 2900 | 0.914 | 0.705 | 1.122 | 3.238 | 3.416 | 1.46e-03 | 3.50e-02 | -1.099 | ubiquitin fusion degradation protein 1, putative | UFD1 |
| 4 | PF3D7_0101000 | Pf3D7_01_v3 | 65817 | - | 1173 | -2.291 | -3.297 | -1.284 | -1.114 | -3.415 | 1.48e-03 | 3.50e-02 | -1.198 | rifin | RIF |
| 162 | PF3D7_0700100 | Pf3D7_07_v3 | 20307 | + | 7777 | -1.047 | -1.695 | -0.399 | 5.134 | -3.416 | 1.47e-03 | 3.50e-02 | -1.202 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 197 | PF3D7_0733000 | Pf3D7_07_v3 | 1417588 | - | 8647 | -0.963 | -1.570 | -0.355 | 4.915 | -3.408 | 1.49e-03 | 3.51e-02 | -1.201 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 85 | PF3D7_0501300 | Pf3D7_05_v3 | 68930 | + | 1184 | -0.878 | -1.677 | -0.078 | 12.513 | -3.409 | 1.54e-03 | 3.60e-02 | -1.464 | skeleton-binding protein 1 | SBP1 |
| 366 | PF3D7_1200200 | Pf3D7_12_v3 | 26321 | - | 1367 | -1.905 | -2.207 | -1.603 | -0.371 | -3.395 | 1.55e-03 | 3.61e-02 | -1.192 | rifin | RIF |
| 181 | PF3D7_0713500 | Pf3D7_07_v3 | 614385 | + | 2865 | 0.993 | 0.415 | 1.570 | 4.315 | 3.384 | 1.60e-03 | 3.70e-02 | -1.219 | conserved Plasmodium protein, unknown function | NA |
| 36 | PF3D7_0304900 | Pf3D7_03_v3 | 231793 | - | 513 | 0.815 | -0.110 | 1.740 | 5.014 | 3.381 | 1.61e-03 | 3.71e-02 | -1.273 | conserved Plasmodium protein, unknown function | NA |
| 507 | PF3D7_1404900 | Pf3D7_14_v3 | 170000 | + | 894 | 0.417 | -0.160 | 0.993 | 8.339 | 3.377 | 1.63e-03 | 3.73e-02 | -1.509 | conserved Plasmodium protein, unknown function | NA |
| 81 | PF3D7_0423800 | Pf3D7_04_v3 | 1076347 | + | 1188 | 1.880 | 1.141 | 2.620 | 2.150 | 3.388 | 1.64e-03 | 3.73e-02 | -1.171 | cysteine-rich protective antigen | CyRPA |
| 271 | PF3D7_0935900 | Pf3D7_09_v3 | 1420483 | - | 2325 | -0.731 | -1.228 | -0.234 | 13.774 | -3.374 | 1.66e-03 | 3.74e-02 | -1.525 | ring-exported protein 1 | REX1 |
| 437 | PF3D7_1304300 | Pf3D7_13_v3 | 231083 | + | 642 | 1.450 | 1.125 | 1.775 | 0.470 | 3.370 | 1.66e-03 | 3.74e-02 | -1.206 | conserved Plasmodium protein, unknown function | NA |
| 539 | PF3D7_1436500 | Pf3D7_14_v3 | 1488706 | + | 1296 | 1.168 | 0.522 | 1.814 | 0.239 | 3.368 | 1.67e-03 | 3.74e-02 | -1.221 | GTP-binding protein, putative | NA |
| 311 | PF3D7_1037100 | Pf3D7_10_v3 | 1469990 | - | 2238 | -0.903 | -1.216 | -0.591 | 3.447 | -3.364 | 1.69e-03 | 3.77e-02 | -1.259 | pyruvate kinase 2 | PyKII |
| 451 | PF3D7_1321600 | Pf3D7_13_v3 | 897716 | + | 3329 | 1.222 | 0.430 | 2.014 | 0.168 | 3.360 | 1.71e-03 | 3.79e-02 | -1.239 | phosphodiesterase gamma, putative | PDEgamma |
| 16 | PF3D7_0202400 | Pf3D7_02_v3 | 120524 | + | 3579 | -1.206 | -1.524 | -0.888 | 4.276 | -3.344 | 1.81e-03 | 3.86e-02 | -1.339 | gamete antigen 27/25, putative | NA |
| 74 | PF3D7_0417400 | Pf3D7_04_v3 | 756294 | + | 20310 | -0.713 | -1.449 | 0.023 | 8.087 | -3.340 | 1.82e-03 | 3.86e-02 | -1.599 | conserved Plasmodium protein, unknown function | NA |
| 141 | PF3D7_0609700 | Pf3D7_06_v3 | 413652 | + | 6130 | -0.601 | -0.938 | -0.263 | 9.580 | -3.340 | 1.81e-03 | 3.86e-02 | -1.625 | conserved Plasmodium protein, unknown function | NA |
| 183 | PF3D7_0714600 | Pf3D7_07_v3 | 667985 | + | 1728 | -0.631 | -1.087 | -0.175 | 6.973 | -3.344 | 1.79e-03 | 3.86e-02 | -1.529 | conserved Plasmodium protein, unknown function | NA |
| 268 | PF3D7_0932900 | Pf3D7_09_v3 | 1309467 | - | 477 | 0.916 | 0.639 | 1.193 | 2.111 | 3.346 | 1.78e-03 | 3.86e-02 | -1.246 | conserved Plasmodium protein, unknown function | NA |
| 323 | PF3D7_1106300 | Pf3D7_11_v3 | 263604 | - | 2967 | -1.016 | -1.287 | -0.745 | 4.205 | -3.344 | 1.79e-03 | 3.86e-02 | -1.351 | exonuclease, putative | NA |
| 404 | PF3D7_1235300 | Pf3D7_12_v3 | 1470713 | + | 4989 | -0.615 | -1.360 | 0.131 | 9.308 | -3.345 | 1.78e-03 | 3.86e-02 | -1.612 | CCR4-NOT transcription complex subunit 4, putative | NOT4 |
| 488 | PF3D7_1362300 | Pf3D7_13_v3 | 2493143 | + | 570 | 0.821 | 0.583 | 1.059 | 3.690 | 3.345 | 1.78e-03 | 3.86e-02 | -1.286 | conserved protein, unknown function | NA |
| 167 | PF3D7_0705600 | Pf3D7_07_v3 | 281035 | - | 3399 | 0.942 | 0.430 | 1.454 | 4.013 | 3.337 | 1.83e-03 | 3.86e-02 | -1.317 | RNA helicase, putative | NA |
| 246 | PF3D7_0907700 | Pf3D7_09_v3 | 364069 | - | 840 | 0.428 | -1.470 | 2.326 | 7.924 | 3.334 | 1.84e-03 | 3.87e-02 | -1.609 | subunit of proteaseome activator complex, putative | PA28 |
| 584 | PF3D7_1474500 | Pf3D7_14_v3 | 3055715 | - | 2106 | 0.645 | 0.215 | 1.076 | 6.705 | 3.332 | 1.85e-03 | 3.87e-02 | -1.546 | splicing factor 3A subunit 1, putative | SF3A1 |
| 499 | PF3D7_1400100 | Pf3D7_14_v3 | 1393 | + | 3951 | -1.493 | -1.875 | -1.110 | 4.800 | -3.348 | 1.87e-03 | 3.89e-02 | -1.384 | erythrocyte membrane protein 1 (PfEMP1), pseudogene | NA |
| 18 | PF3D7_0205400 | Pf3D7_02_v3 | 223478 | + | 1374 | 0.422 | -0.097 | 0.941 | 6.151 | 3.315 | 1.94e-03 | 3.98e-02 | -1.545 | PCI domain-containing protein, putative | NA |
| 86 | PF3D7_0501400 | Pf3D7_05_v3 | 74509 | + | 5334 | -1.103 | -2.383 | 0.176 | 11.055 | -3.342 | 1.93e-03 | 3.98e-02 | -1.668 | interspersed repeat antigen | FIRA |
| 145 | PF3D7_0614200 | Pf3D7_06_v3 | 593172 | - | 2733 | 0.977 | 0.171 | 1.784 | 3.935 | 3.317 | 1.93e-03 | 3.98e-02 | -1.364 | cytosolic Fe-S cluster assembly factor NAR1, putative | NAR1 |
| 453 | PF3D7_1322100 | Pf3D7_13_v3 | 920971 | + | 8479 | -0.565 | -1.024 | -0.106 | 9.373 | -3.302 | 2.01e-03 | 4.09e-02 | -1.718 | histone-lysine N-methyltransferase SET2 | SET2 |
| 493 | PF3D7_1366000 | Pf3D7_13_v3 | 2635213 | + | 276 | 1.199 | 0.915 | 1.482 | 2.200 | 3.300 | 2.02e-03 | 4.09e-02 | -1.356 | conserved Plasmodium protein, unknown function | NA |
| 506 | PF3D7_1404700 | Pf3D7_14_v3 | 161227 | - | 873 | 1.202 | 0.598 | 1.806 | 1.784 | 3.300 | 2.02e-03 | 4.09e-02 | -1.353 | conserved Plasmodium protein, unknown function | NA |
| 170 | PF3D7_0707900 | Pf3D7_07_v3 | 366929 | + | 780 | -0.462 | -1.432 | 0.507 | 7.539 | -3.297 | 2.04e-03 | 4.09e-02 | -1.686 | ribosomal protein S8e, putative | NA |
| 234 | PF3D7_0831400 | Pf3D7_08_v3 | 1344405 | - | 1083 | -1.175 | -1.535 | -0.815 | 3.211 | -3.300 | 2.04e-03 | 4.09e-02 | -1.425 | Plasmodium exported protein, unknown function | NA |
| 411 | PF3D7_1244100 | Pf3D7_12_v3 | 1847677 | + | 4480 | -0.527 | -1.212 | 0.158 | 5.926 | -3.294 | 2.06e-03 | 4.10e-02 | -1.589 | N-alpha-acetyltransferase 15, NatA auxiliary subunit, putative | NA |
| 52 | PF3D7_0323000 | Pf3D7_03_v3 | 968675 | - | 528 | -0.921 | -1.365 | -0.477 | 4.328 | -3.289 | 2.09e-03 | 4.12e-02 | -1.490 | translation machinery-associated protein 7, putative | TMA7 |
| 106 | PF3D7_0518300 | Pf3D7_05_v3 | 759831 | - | 1168 | -0.466 | -1.340 | 0.407 | 6.608 | -3.289 | 2.09e-03 | 4.12e-02 | -1.653 | proteasome subunit beta type-1, putative | NA |
| 7 | PF3D7_0108500 | Pf3D7_01_v3 | 349170 | + | 540 | -0.889 | -2.271 | 0.492 | 10.229 | -3.295 | 2.13e-03 | 4.17e-02 | -1.766 | conserved Plasmodium protein, unknown function | NA |
| 528 | PF3D7_1424500 | Pf3D7_14_v3 | 979464 | + | 142 | -0.859 | -1.122 | -0.596 | 3.564 | -3.280 | 2.14e-03 | 4.17e-02 | -1.432 | small nucleolar RNA snoR27 | NA |
| 557 | PF3D7_1450300 | Pf3D7_14_v3 | 2056641 | + | 2598 | 0.854 | 0.553 | 1.154 | 5.203 | 3.280 | 2.14e-03 | 4.17e-02 | -1.564 | NADPH–cytochrome P450 reductase, putative | CPR |
| 551 | PF3D7_1446300 | Pf3D7_14_v3 | 1898351 | + | 3576 | 1.201 | 0.852 | 1.550 | 4.099 | 3.281 | 2.16e-03 | 4.19e-02 | -1.484 | conserved Plasmodium membrane protein, unknown function | NA |
| 260 | PF3D7_0923100 | Pf3D7_09_v3 | 941830 | - | 669 | 1.038 | 0.081 | 1.995 | 1.285 | 3.274 | 2.18e-03 | 4.19e-02 | -1.416 | OTU domain-containing protein, putative | NA |
| 184 | PF3D7_0716000 | Pf3D7_07_v3 | 703207 | + | 3378 | -0.470 | -1.219 | 0.279 | 8.598 | -3.270 | 2.20e-03 | 4.21e-02 | -1.798 | RNA-binding protein, putative | NA |
| 427 | PF3D7_1251400 | Pf3D7_12_v3 | 2097436 | - | 1410 | 1.030 | 0.435 | 1.624 | 1.677 | 3.269 | 2.21e-03 | 4.21e-02 | -1.426 | conserved Plasmodium protein, unknown function | NA |
| 554 | PF3D7_1447200 | Pf3D7_14_v3 | 1933985 | + | 1791 | -0.466 | -1.058 | 0.127 | 7.823 | -3.262 | 2.25e-03 | 4.28e-02 | -1.791 | conserved Plasmodium protein, unknown function | NA |
| 402 | PF3D7_1233100 | Pf3D7_12_v3 | 1359169 | + | 408 | -0.816 | -1.368 | -0.264 | 4.139 | -3.251 | 2.32e-03 | 4.33e-02 | -1.536 | conserved protein, unknown function | NA |
| 532 | PF3D7_1427200 | Pf3D7_14_v3 | 1061805 | + | 975 | -1.510 | -1.777 | -1.242 | 1.616 | -3.254 | 2.32e-03 | 4.33e-02 | -1.470 | selenoprotein | Sel4 |
| 544 | PF3D7_1440200 | Pf3D7_14_v3 | 1639477 | + | 7691 | -0.893 | -1.631 | -0.155 | 1.898 | -3.256 | 2.29e-03 | 4.33e-02 | -1.464 | stromal-processing peptidase, putative | SPP |
| 586 | PF3D7_1476200 | Pf3D7_14_v3 | 3133951 | + | 1701 | -1.328 | -1.802 | -0.855 | 6.583 | -3.275 | 2.32e-03 | 4.33e-02 | -1.685 | Plasmodium exported protein (PHISTb), unknown function | NA |
| 248 | PF3D7_0909600 | Pf3D7_09_v3 | 433238 | - | 2136 | 1.309 | 0.280 | 2.338 | 0.859 | 3.247 | 2.34e-03 | 4.36e-02 | -1.483 | conserved Plasmodium protein, unknown function | NA |
| 231 | PF3D7_0829100 | Pf3D7_08_v3 | 1252349 | + | 1448 | -0.507 | -1.092 | 0.079 | 7.094 | -3.237 | 2.41e-03 | 4.46e-02 | -1.817 | conserved protein, unknown function | NA |
| 103 | PF3D7_0517100 | Pf3D7_05_v3 | 718425 | - | 1431 | 1.003 | 0.547 | 1.459 | 3.663 | 3.233 | 2.44e-03 | 4.47e-02 | -1.555 | conserved Plasmodium protein, unknown function | NA |
| 283 | PF3D7_1011800 | Pf3D7_10_v3 | 455398 | + | 3420 | -0.582 | -1.221 | 0.058 | 10.650 | -3.234 | 2.43e-03 | 4.47e-02 | -1.910 | PRE-binding protein | PREBP |
| 19 | PF3D7_0208200 | Pf3D7_02_v3 | 335679 | - | 903 | -0.382 | -0.905 | 0.140 | 7.526 | -3.227 | 2.48e-03 | 4.51e-02 | -1.866 | KRR1 small subunit processome component, putative | KRR1 |
| 136 | PF3D7_0605100 | Pf3D7_06_v3 | 217240 | + | 2268 | 0.892 | 0.414 | 1.370 | 6.752 | 3.231 | 2.50e-03 | 4.51e-02 | -1.816 | RNA-binding protein, putative | NA |
| 400 | PF3D7_1231600 | Pf3D7_12_v3 | 1301098 | - | 3507 | -0.662 | -1.473 | 0.148 | 6.353 | -3.224 | 2.50e-03 | 4.51e-02 | -1.800 | pre-mRNA-splicing factor ATP-dependent RNA helicase PRP2, putative | PRP2 |
| 479 | PF3D7_1353500 | Pf3D7_13_v3 | 2144125 | + | 981 | 0.792 | 0.198 | 1.385 | 3.058 | 3.228 | 2.48e-03 | 4.51e-02 | -1.552 | RNA polymerase II transcription factor B subunit 4, putative | TFB4 |
| 578 | PF3D7_1468100 | Pf3D7_14_v3 | 2786308 | - | 8016 | -0.518 | -1.168 | 0.132 | 10.232 | -3.221 | 2.52e-03 | 4.53e-02 | -1.941 | conserved Plasmodium protein, unknown function | NA |
| 46 | PF3D7_0317900 | Pf3D7_03_v3 | 739428 | + | 2306 | 0.832 | 0.540 | 1.124 | 2.115 | 3.209 | 2.61e-03 | 4.61e-02 | -1.571 | conserved Plasmodium protein, unknown function | NA |
| 188 | PF3D7_0719500 | Pf3D7_07_v3 | 854652 | - | 2003 | 0.901 | 0.216 | 1.586 | 1.522 | 3.208 | 2.61e-03 | 4.61e-02 | -1.569 | LEM3/CDC50 family protein, putative | NA |
| 254 | PF3D7_0915500 | Pf3D7_09_v3 | 657418 | + | 1995 | 1.209 | 0.535 | 1.884 | 0.043 | 3.211 | 2.59e-03 | 4.61e-02 | -1.579 | conserved Plasmodium protein, unknown function | NA |
| 566 | PF3D7_1457100 | Pf3D7_14_v3 | 2340784 | + | 2244 | -1.001 | -1.317 | -0.685 | 6.569 | -3.223 | 2.59e-03 | 4.61e-02 | -1.819 | conserved Plasmodium protein, unknown function | NA |
| 355 | PF3D7_1137300 | Pf3D7_11_v3 | 1466197 | - | 2070 | 0.417 | 0.046 | 0.787 | 7.338 | 3.205 | 2.63e-03 | 4.62e-02 | -1.909 | CLPTM1 domain-containing protein, putative | NA |
| 112 | PF3D7_0521000 | Pf3D7_05_v3 | 859373 | - | 1691 | -0.642 | -1.091 | -0.193 | 6.047 | -3.202 | 2.66e-03 | 4.62e-02 | -1.821 | conserved Plasmodium protein, unknown function | NA |
| 126 | PF3D7_0528100 | Pf3D7_05_v3 | 1157840 | - | 3714 | -0.403 | -1.040 | 0.233 | 9.336 | -3.204 | 2.65e-03 | 4.62e-02 | -1.981 | AP-1 complex subunit beta, putative | NA |
| 529 | PF3D7_1426000 | Pf3D7_14_v3 | 1016133 | - | 486 | 0.507 | -0.016 | 1.030 | 8.634 | 3.198 | 2.69e-03 | 4.66e-02 | -1.980 | 60S ribosomal protein L21 | RPL21 |
| 88 | PF3D7_0502500 | Pf3D7_05_v3 | 114149 | + | 1785 | 1.651 | 0.516 | 2.786 | 0.248 | 3.195 | 2.71e-03 | 4.67e-02 | -1.609 | conserved Plasmodium protein, unknown function | NA |
| 169 | PF3D7_0707800 | Pf3D7_07_v3 | 362005 | + | 3775 | 0.725 | 0.305 | 1.145 | 2.258 | 3.191 | 2.74e-03 | 4.67e-02 | -1.614 | RAP protein, putative | NA |
| 176 | PF3D7_0709600 | Pf3D7_07_v3 | 429857 | - | 3902 | -0.469 | -1.245 | 0.307 | 7.336 | -3.192 | 2.73e-03 | 4.67e-02 | -1.943 | ribonucleases P/MRP protein subunit POP1, putative | POP1 |
| 494 | PF3D7_1366500 | Pf3D7_13_v3 | 2661573 | + | 450 | 1.113 | 0.527 | 1.698 | 0.692 | 3.194 | 2.72e-03 | 4.67e-02 | -1.606 | nucleoside diphosphate kinase | NDK |
| 380 | PF3D7_1214300 | Pf3D7_12_v3 | 608542 | - | 1472 | 0.720 | 0.483 | 0.958 | 3.646 | 3.185 | 2.79e-03 | 4.73e-02 | -1.676 | geranylgeranyl transferase type2 beta subunit, putative | NA |
| 436 | PF3D7_1303100 | Pf3D7_13_v3 | 159024 | + | 892 | -0.803 | -2.210 | 0.604 | 3.666 | -3.183 | 2.80e-03 | 4.74e-02 | -1.711 | methyltransferase-like protein, putative | NA |
| 30 | PF3D7_0300100 | Pf3D7_03_v3 | 36965 | + | 7518 | -0.916 | -1.729 | -0.104 | 4.393 | -3.180 | 2.83e-03 | 4.76e-02 | -1.739 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 2 | mal_rna_17:rRNA | M76611 | 5577 | - | 195 | -1.367 | -1.613 | -1.121 | 4.213 | -3.186 | 2.84e-03 | 4.77e-02 | -1.707 | NA | NA |
| 351 | PF3D7_1133700 | Pf3D7_11_v3 | 1302173 | + | 3815 | -0.628 | -0.975 | -0.282 | 10.101 | -3.173 | 2.88e-03 | 4.77e-02 | -2.061 | FHA domain-containing protein, putative | NA |
| 352 | PF3D7_1134800 | Pf3D7_11_v3 | 1367186 | + | 1624 | 0.455 | -0.083 | 0.993 | 6.513 | 3.172 | 2.89e-03 | 4.77e-02 | -1.940 | coatomer subunit delta | NA |
| 484 | PF3D7_1359100 | Pf3D7_13_v3 | 2347863 | - | 2124 | 0.651 | 0.215 | 1.087 | 4.613 | 3.172 | 2.89e-03 | 4.77e-02 | -1.776 | riboflavin kinase / FAD synthase family protein, putative | NA |
| 526 | PF3D7_1421600 | Pf3D7_14_v3 | 885211 | + | 2660 | 0.487 | -0.563 | 1.537 | 5.100 | 3.175 | 2.86e-03 | 4.77e-02 | -1.811 | conserved Plasmodium protein, unknown function | NA |
| 536 | PF3D7_1434300 | Pf3D7_14_v3 | 1372903 | + | 1695 | -0.405 | -0.857 | 0.047 | 8.758 | -3.168 | 2.92e-03 | 4.80e-02 | -2.063 | Hsp70/Hsp90 organizing protein | HOP |
| 118 | PF3D7_0523700 | Pf3D7_05_v3 | 980754 | - | 4601 | 1.400 | 1.030 | 1.771 | 0.959 | 3.166 | 2.93e-03 | 4.80e-02 | -1.665 | conserved Plasmodium membrane protein, unknown function | NA |
| 305 | PF3D7_1027300 | Pf3D7_10_v3 | 1140589 | - | 2014 | -0.778 | -1.652 | 0.097 | 8.553 | -3.169 | 2.96e-03 | 4.83e-02 | -2.054 | peroxiredoxin | nPrx |
| 39 | PF3D7_0310800 | Pf3D7_03_v3 | 464662 | + | 330 | 0.432 | -0.360 | 1.224 | 6.118 | 3.148 | 3.08e-03 | 4.83e-02 | -1.965 | conserved Plasmodium protein, unknown function | NA |
| 44 | PF3D7_0317100 | Pf3D7_03_v3 | 686282 | + | 3201 | 0.881 | 0.224 | 1.538 | 2.554 | 3.153 | 3.04e-03 | 4.83e-02 | -1.711 | 6-cysteine protein | B9 |
| 125 | PF3D7_0528000 | Pf3D7_05_v3 | 1156205 | - | 375 | 0.842 | 0.497 | 1.187 | 3.660 | 3.148 | 3.09e-03 | 4.83e-02 | -1.767 | proteasome maturation factor UMP1, putative | UMP1 |
| 221 | PF3D7_0821600 | Pf3D7_08_v3 | 969690 | + | 2025 | 0.546 | 0.255 | 0.836 | 6.666 | 3.160 | 2.98e-03 | 4.83e-02 | -1.983 | clp1-related protein, putative | NA |
| 267 | PF3D7_0931400 | Pf3D7_09_v3 | 1263347 | + | 1484 | -0.833 | -1.433 | -0.232 | 3.619 | -3.147 | 3.09e-03 | 4.83e-02 | -1.764 | conserved Plasmodium protein, unknown function | NA |
| 316 | PF3D7_1102700 | Pf3D7_11_v3 | 128789 | + | 276 | -0.581 | -0.941 | -0.221 | 10.495 | -3.158 | 3.00e-03 | 4.83e-02 | -2.103 | early transcribed membrane protein 11.1 | ETRAMP11.1 |
| 328 | PF3D7_1111000 | Pf3D7_11_v3 | 434802 | + | 1740 | 0.567 | -0.232 | 1.365 | 5.346 | 3.155 | 3.03e-03 | 4.83e-02 | -1.879 | tRNA m5C-methyltransferase, putative | NA |
| 420 | PF3D7_1247900 | Pf3D7_12_v3 | 1972438 | + | 639 | -0.619 | -1.165 | -0.073 | 6.344 | -3.158 | 3.00e-03 | 4.83e-02 | -1.955 | nucleolar rRNA processing protein, putative | NA |
| 446 | PF3D7_1315800 | Pf3D7_13_v3 | 660018 | - | 1245 | 0.590 | 0.115 | 1.066 | 5.323 | 3.152 | 3.05e-03 | 4.83e-02 | -1.879 | transcription factor MYB1 | MYB1 |
| 481 | PF3D7_1355200 | Pf3D7_13_v3 | 2191058 | - | 3054 | 1.714 | 1.217 | 2.211 | 0.476 | 3.158 | 3.02e-03 | 4.83e-02 | -1.693 | RAP protein, putative | NA |
| 485 | PF3D7_1360100 | Pf3D7_13_v3 | 2405249 | - | 969 | -0.542 | -1.093 | 0.009 | 5.548 | -3.149 | 3.07e-03 | 4.83e-02 | -1.907 | RNA-binding protein, putative | NA |
| 76 | PF3D7_0418300 | Pf3D7_04_v3 | 819362 | - | 2979 | 0.592 | -0.214 | 1.398 | 10.491 | 3.142 | 3.13e-03 | 4.88e-02 | -2.141 | conserved Plasmodium protein, unknown function | NA |
| 66 | PF3D7_0409900 | Pf3D7_04_v3 | 461991 | - | 1967 | 0.910 | 0.534 | 1.286 | 2.782 | 3.138 | 3.17e-03 | 4.91e-02 | -1.752 | actin-like protein, putative | ALP5b |
| 440 | PF3D7_1306700 | Pf3D7_13_v3 | 318332 | - | 1404 | 1.059 | 0.686 | 1.433 | 0.096 | 3.137 | 3.18e-03 | 4.92e-02 | -1.744 | conserved Plasmodium protein, unknown function | NA |
| 164 | PF3D7_0703200 | Pf3D7_07_v3 | 122513 | - | 4623 | -0.952 | -1.551 | -0.353 | 4.482 | -3.133 | 3.21e-03 | 4.94e-02 | -1.873 | conserved Plasmodium protein, unknown function | NA |
| 308 | PF3D7_1030100 | Pf3D7_10_v3 | 1224519 | - | 4574 | -0.400 | -0.931 | 0.130 | 8.748 | -3.130 | 3.24e-03 | 4.98e-02 | -2.159 | pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22, putative | PRP22 |
| 358 | PF3D7_1140800 | Pf3D7_11_v3 | 1633920 | + | 2412 | 0.466 | -0.235 | 1.166 | 6.642 | 3.127 | 3.27e-03 | 5.00e-02 | -2.059 | conserved Plasmodium protein, unknown function | NA |
| 542 | PF3D7_1438500 | Pf3D7_14_v3 | 1557527 | - | 2631 | 0.561 | 0.255 | 0.868 | 6.161 | 3.124 | 3.29e-03 | 5.01e-02 | -2.028 | cleavage and polyadenylation specificity factor subunit 3, putative | CPSF3 |
| 54 | PF3D7_0324900 | Pf3D7_03_v3 | 1030822 | - | 7433 | -0.994 | -1.486 | -0.503 | 4.088 | -3.114 | 3.38e-03 | 5.09e-02 | -1.874 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 185 | PF3D7_0717200 | Pf3D7_07_v3 | 745191 | - | 1473 | -1.486 | -1.798 | -1.174 | 6.245 | -3.143 | 3.39e-03 | 5.09e-02 | -2.041 | conserved Plasmodium protein, unknown function | NA |
| 350 | PF3D7_1133000 | Pf3D7_11_v3 | 1275574 | + | 90 | 1.218 | 0.798 | 1.639 | 0.916 | 3.117 | 3.36e-03 | 5.09e-02 | -1.777 | conserved Plasmodium protein, unknown function | NA |
| 471 | PF3D7_1346400 | Pf3D7_13_v3 | 1852898 | + | 17967 | -0.515 | -1.373 | 0.343 | 7.880 | -3.116 | 3.37e-03 | 5.09e-02 | -2.164 | conserved Plasmodium protein, unknown function | NA |
| 139 | PF3D7_0607000 | Pf3D7_06_v3 | 293864 | + | 2934 | -0.455 | -0.867 | -0.043 | 10.493 | -3.110 | 3.42e-03 | 5.10e-02 | -2.226 | translation initiation factor IF-2, putative | NA |
| 478 | PF3D7_1353300 | Pf3D7_13_v3 | 2132068 | - | 6516 | -0.559 | -0.936 | -0.182 | 4.337 | -3.110 | 3.42e-03 | 5.10e-02 | -1.917 | conserved Plasmodium protein, unknown function | NA |
| 338 | PF3D7_1122300 | Pf3D7_11_v3 | 846929 | + | 1086 | 0.930 | 0.523 | 1.338 | 3.822 | 3.108 | 3.44e-03 | 5.11e-02 | -1.877 | conserved Plasmodium protein, unknown function | NA |
| 168 | PF3D7_0707700 | Pf3D7_07_v3 | 357700 | + | 2886 | 0.405 | -0.286 | 1.095 | 7.727 | 3.103 | 3.49e-03 | 5.16e-02 | -2.191 | E3 ubiquitin-protein ligase, putative | NA |
| 313 | PF3D7_1039000 | Pf3D7_10_v3 | 1568709 | + | 3107 | -0.863 | -1.648 | -0.078 | 8.303 | -3.112 | 3.50e-03 | 5.16e-02 | -2.178 | serine/threonine protein kinase, FIKK family | FIKK10.2 |
| 295 | PF3D7_1018300 | Pf3D7_10_v3 | 729809 | - | 3048 | 0.658 | 0.037 | 1.280 | 7.546 | 3.099 | 3.53e-03 | 5.18e-02 | -2.187 | conserved Plasmodium protein, unknown function | NA |
| 298 | PF3D7_1019300 | Pf3D7_10_v3 | 774929 | - | 5559 | 0.836 | 0.550 | 1.123 | 4.343 | 3.098 | 3.54e-03 | 5.18e-02 | -1.925 | zinc finger protein, putative | NA |
| 348 | PF3D7_1131200 | Pf3D7_11_v3 | 1199253 | + | 2553 | -1.295 | -1.897 | -0.693 | 2.053 | -3.094 | 3.59e-03 | 5.24e-02 | -1.861 | conserved Plasmodium protein, unknown function | NA |
| 31 | PF3D7_0300200 | Pf3D7_03_v3 | 46369 | - | 1211 | -1.606 | -2.102 | -1.111 | 0.105 | -3.084 | 3.67e-03 | 5.30e-02 | -1.858 | rifin | RIF |
| 490 | PF3D7_1364300 | Pf3D7_13_v3 | 2579159 | - | 3456 | 0.508 | 0.165 | 0.851 | 6.964 | 3.086 | 3.65e-03 | 5.30e-02 | -2.185 | pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 | PRP16 |
| 516 | PF3D7_1414100 | Pf3D7_14_v3 | 560093 | + | 2232 | 0.593 | -0.128 | 1.314 | 6.951 | 3.085 | 3.67e-03 | 5.30e-02 | -2.185 | conserved Plasmodium protein, unknown function | NA |
| 59 | PF3D7_0404300 | Pf3D7_04_v3 | 234014 | - | 3000 | -0.909 | -1.560 | -0.257 | 7.649 | -3.089 | 3.73e-03 | 5.31e-02 | -2.234 | conserved Plasmodium protein, unknown function | NA |
| 94 | PF3D7_0509800 | Pf3D7_05_v3 | 410268 | + | 5041 | -0.353 | -1.775 | 1.070 | 8.261 | -3.079 | 3.73e-03 | 5.31e-02 | -2.275 | phosphatidylinositol 4-kinase | PI4K |
| 134 | PF3D7_0601600 | Pf3D7_06_v3 | 68833 | - | 861 | 1.190 | 0.854 | 1.527 | 1.022 | 3.079 | 3.72e-03 | 5.31e-02 | -1.861 | tetratricopeptide repeat protein, putative | NA |
| 275 | PF3D7_1002300 | Pf3D7_10_v3 | 117242 | + | 1293 | 0.952 | -0.352 | 2.255 | 1.443 | 3.078 | 3.73e-03 | 5.31e-02 | -1.865 | conserved Plasmodium protein, unknown function | NA |
| 128 | PF3D7_0528800 | Pf3D7_05_v3 | 1180425 | - | 1614 | 0.448 | -0.366 | 1.262 | 6.042 | 3.075 | 3.77e-03 | 5.35e-02 | -2.139 | nucleolar preribosomal GTPase, putative | NA |
| 120 | PF3D7_0524400 | Pf3D7_05_v3 | 1013453 | - | 1098 | 0.865 | 0.219 | 1.511 | 6.191 | 3.074 | 3.81e-03 | 5.39e-02 | -2.157 | ribosome-interacting GTPase 1, putative | RBG1 |
| 258 | PF3D7_0922100 | Pf3D7_09_v3 | 895415 | + | 4890 | -0.473 | -0.673 | -0.274 | 10.500 | -3.069 | 3.83e-03 | 5.39e-02 | -2.327 | ubiquitin-like protein, putative | NA |
| 10 | PF3D7_0115200 | Pf3D7_01_v3 | 591849 | + | 1339 | -2.160 | -2.833 | -1.487 | -0.510 | -3.072 | 3.87e-03 | 5.42e-02 | -1.914 | rifin | RIF |
| 375 | PF3D7_1210300 | Pf3D7_12_v3 | 465115 | + | 630 | 0.735 | 0.280 | 1.189 | 3.502 | 3.066 | 3.86e-03 | 5.42e-02 | -1.955 | conserved Plasmodium protein, unknown function | NA |
| 257 | PF3D7_0921900 | Pf3D7_09_v3 | 888559 | + | 747 | -0.520 | -0.912 | -0.129 | 6.911 | -3.062 | 3.90e-03 | 5.44e-02 | -2.242 | conserved Plasmodium protein, unknown function | NA |
| 349 | PF3D7_1132300 | Pf3D7_11_v3 | 1253073 | + | 822 | 0.867 | 0.243 | 1.491 | 2.387 | 3.059 | 3.93e-03 | 5.47e-02 | -1.929 | nucleic acid binding protein, putative | NA |
| 325 | PF3D7_1108600 | Pf3D7_11_v3 | 369675 | - | 1032 | -0.688 | -1.013 | -0.362 | 9.245 | -3.056 | 4.00e-03 | 5.48e-02 | -2.350 | endoplasmic reticulum-resident calcium binding protein | ERC |
| 346 | PF3D7_1127000 | Pf3D7_11_v3 | 1056198 | - | 1857 | -0.592 | -1.048 | -0.137 | 6.998 | -3.053 | 3.99e-03 | 5.48e-02 | -2.265 | protein phosphatase, putative | NA |
| 464 | PF3D7_1336700 | Pf3D7_13_v3 | 1482361 | - | 477 | 0.629 | 0.304 | 0.955 | 7.531 | 3.056 | 3.97e-03 | 5.48e-02 | -2.291 | conserved Plasmodium protein, unknown function | NA |
| 501 | PF3D7_1401600 | Pf3D7_14_v3 | 61364 | - | 1625 | -0.647 | -1.129 | -0.166 | 8.941 | -3.054 | 4.01e-03 | 5.48e-02 | -2.354 | Plasmodium exported protein (PHISTb), unknown function | NA |
| 560 | PF3D7_1451100 | Pf3D7_14_v3 | 2090902 | + | 2499 | -0.618 | -1.411 | 0.175 | 12.579 | -3.052 | 4.00e-03 | 5.48e-02 | -2.354 | elongation factor 2 | eEF2 |
| 266 | PF3D7_0931000 | Pf3D7_09_v3 | 1248866 | - | 2736 | 1.104 | 0.394 | 1.813 | 2.571 | 3.048 | 4.05e-03 | 5.52e-02 | -1.957 | elongation factor Tu, putative | NA |
| 249 | PF3D7_0913100 | Pf3D7_09_v3 | 571031 | - | 2319 | 1.128 | 0.659 | 1.596 | -0.224 | 3.043 | 4.10e-03 | 5.55e-02 | -1.951 | conserved Plasmodium protein, unknown function | NA |
| 504 | PF3D7_1403900 | Pf3D7_14_v3 | 142242 | - | 897 | -0.742 | -1.681 | 0.197 | 4.660 | -3.043 | 4.10e-03 | 5.55e-02 | -2.132 | serine/threonine protein phosphatase CPPED1, putative | CPPED1 |
| 217 | PF3D7_0818000 | Pf3D7_08_v3 | 821334 | + | 1119 | 0.720 | 0.222 | 1.219 | 6.278 | 3.041 | 4.12e-03 | 5.56e-02 | -2.236 | conserved protein, unknown function | NA |
| 363 | PF3D7_1149200 | Pf3D7_11_v3 | 1976407 | + | 3398 | -1.041 | -1.909 | -0.173 | 9.787 | -3.056 | 4.18e-03 | 5.63e-02 | -2.356 | ring-infected erythrocyte surface antigen | NA |
| 337 | PF3D7_1121600 | Pf3D7_11_v3 | 815386 | - | 937 | -0.509 | -1.042 | 0.024 | 10.612 | -3.032 | 4.23e-03 | 5.67e-02 | -2.420 | exported protein 1 | EXP1 |
| 531 | PF3D7_1426200 | Pf3D7_14_v3 | 1021652 | - | 1206 | -0.447 | -0.794 | -0.101 | 7.961 | -3.027 | 4.28e-03 | 5.72e-02 | -2.389 | protein arginine N-methyltransferase 1 | PRMT1 |
| 392 | PF3D7_1225200 | Pf3D7_12_v3 | 1024455 | - | 3564 | 0.388 | -0.237 | 1.013 | 6.864 | 3.023 | 4.33e-03 | 5.77e-02 | -2.334 | conserved Plasmodium protein, unknown function | NA |
| 373 | PF3D7_1207100 | Pf3D7_12_v3 | 324336 | - | 2523 | -0.473 | -0.846 | -0.100 | 8.689 | -3.017 | 4.40e-03 | 5.82e-02 | -2.438 | small subunit rRNA processing factor, putative | NA |
| 450 | PF3D7_1319300 | Pf3D7_13_v3 | 795939 | - | 2415 | 0.353 | -0.504 | 1.210 | 7.942 | 3.017 | 4.40e-03 | 5.82e-02 | -2.407 | N2,N2-dimethylguanosine tRNA methyltransferase, putative | NA |
| 143 | PF3D7_0612900 | Pf3D7_06_v3 | 531126 | + | 2061 | -0.376 | -1.106 | 0.354 | 9.170 | -3.014 | 4.44e-03 | 5.86e-02 | -2.456 | nucleolar GTP-binding protein 1, putative | NA |
| 83 | PF3D7_0424900 | Pf3D7_04_v3 | 1127779 | + | 1024 | -0.621 | -1.267 | 0.026 | 8.713 | -3.004 | 4.56e-03 | 5.97e-02 | -2.459 | Plasmodium exported protein (PHISTa), unknown function | NA |
| 108 | PF3D7_0518500 | Pf3D7_05_v3 | 763532 | - | 3372 | -0.459 | -1.062 | 0.143 | 8.229 | -3.006 | 4.54e-03 | 5.97e-02 | -2.454 | ATP-dependent RNA helicase DDX23, putative | DDX23 |
| 300 | PF3D7_1022400 | Pf3D7_10_v3 | 939938 | - | 2297 | -0.623 | -0.877 | -0.369 | 9.102 | -3.005 | 4.56e-03 | 5.97e-02 | -2.478 | serine/arginine-rich splicing factor 4 | SRSF4 |
| 189 | PF3D7_0720200 | Pf3D7_07_v3 | 879454 | + | 493 | -0.541 | -1.480 | 0.398 | 4.827 | -3.001 | 4.59e-03 | 5.98e-02 | -2.202 | conserved Plasmodium protein, unknown function | NA |
| 284 | PF3D7_1012000 | Pf3D7_10_v3 | 463493 | + | 3514 | -0.531 | -0.908 | -0.154 | 6.112 | -2.998 | 4.63e-03 | 5.99e-02 | -2.336 | E3 ubiquitin-protein ligase, putative | NA |
| 287 | PF3D7_1014700 | Pf3D7_10_v3 | 595308 | + | 915 | -0.767 | -1.076 | -0.458 | 3.527 | -2.997 | 4.64e-03 | 5.99e-02 | -2.168 | prohibitin, putative | NA |
| 401 | PF3D7_1232200 | Pf3D7_12_v3 | 1333134 | + | 1763 | -0.964 | -1.289 | -0.639 | 0.873 | -2.996 | 4.65e-03 | 5.99e-02 | -2.047 | dihydrolipoyl dehydrogenase, mitochondrial | LPD1 |
| 572 | PF3D7_1460500 | Pf3D7_14_v3 | 2466091 | + | 4899 | 0.945 | -0.112 | 2.003 | 2.462 | 2.996 | 4.66e-03 | 5.99e-02 | -2.071 | conserved Plasmodium protein, unknown function | NA |
| 282 | PF3D7_1009900 | Pf3D7_10_v3 | 399207 | + | 2572 | 0.775 | 0.279 | 1.272 | 3.916 | 2.990 | 4.73e-03 | 6.07e-02 | -2.156 | conserved Plasmodium protein, unknown function | NA |
| 37 | PF3D7_0305000 | Pf3D7_03_v3 | 234058 | - | 1277 | 0.734 | 0.417 | 1.051 | 3.430 | 2.985 | 4.79e-03 | 6.09e-02 | -2.158 | elongation factor Ts | EF-Ts |
| 70 | PF3D7_0415300 | Pf3D7_04_v3 | 681810 | + | 4159 | -0.512 | -0.922 | -0.103 | 8.667 | -2.986 | 4.78e-03 | 6.09e-02 | -2.513 | cdc2-related protein kinase 3 | CRK3 |
| 496 | PF3D7_1368500 | Pf3D7_13_v3 | 2722690 | + | 2493 | 1.037 | 0.748 | 1.325 | 0.223 | 2.985 | 4.79e-03 | 6.09e-02 | -2.070 | conserved Plasmodium protein, unknown function | NA |
| 376 | PF3D7_1211000 | Pf3D7_12_v3 | 484065 | + | 5838 | -1.213 | -1.654 | -0.773 | 0.530 | -2.983 | 4.82e-03 | 6.11e-02 | -2.073 | kinesin-7, putative | NA |
| 233 | PF3D7_0830900 | Pf3D7_08_v3 | 1317600 | - | 742 | -0.885 | -1.343 | -0.426 | 4.631 | -2.983 | 4.84e-03 | 6.11e-02 | -2.271 | Plasmodium exported protein, unknown function | NA |
| 263 | PF3D7_0926000 | Pf3D7_09_v3 | 1043542 | + | 4253 | 0.754 | -0.393 | 1.900 | 3.345 | 2.981 | 4.85e-03 | 6.11e-02 | -2.140 | protein kinase, putative | NA |
| 312 | PF3D7_1037900 | Pf3D7_10_v3 | 1502955 | - | 1368 | 0.957 | 0.577 | 1.338 | 2.108 | 2.975 | 4.92e-03 | 6.18e-02 | -2.115 | conserved Plasmodium protein, unknown function | NA |
| 51 | PF3D7_0321000 | Pf3D7_03_v3 | 877735 | + | 1777 | -0.811 | -1.143 | -0.479 | 4.629 | -2.970 | 4.99e-03 | 6.23e-02 | -2.252 | conserved Plasmodium protein, unknown function | NA |
| 384 | PF3D7_1217000 | Pf3D7_12_v3 | 674349 | - | 429 | 0.921 | 0.367 | 1.475 | 1.664 | 2.970 | 4.99e-03 | 6.23e-02 | -2.111 | conserved Plasmodium protein, unknown function | NA |
| 385 | PF3D7_1217300 | Pf3D7_12_v3 | 682837 | + | 2886 | 0.667 | 0.061 | 1.273 | 6.184 | 2.965 | 5.05e-03 | 6.25e-02 | -2.409 | GTP-binding protein, putative | NA |
| 410 | PF3D7_1243900 | Pf3D7_12_v3 | 1834064 | - | 6673 | -1.332 | -1.711 | -0.953 | 0.596 | -2.965 | 5.05e-03 | 6.25e-02 | -2.111 | double C2-like domain-containing protein | DOC2 |
| 434 | PF3D7_1302900 | Pf3D7_13_v3 | 154992 | + | 2403 | 0.967 | 0.329 | 1.604 | 3.551 | 2.965 | 5.05e-03 | 6.25e-02 | -2.203 | conserved Plasmodium protein, unknown function | NA |
| 429 | PF3D7_1253100 | Pf3D7_12_v3 | 2171342 | + | 1008 | 0.565 | -0.066 | 1.197 | 6.955 | 2.961 | 5.10e-03 | 6.29e-02 | -2.491 | Plasmodium exported protein (PHISTa), unknown function | NA |
| 27 | PF3D7_0220300 | Pf3D7_02_v3 | 813827 | - | 828 | -1.012 | -1.660 | -0.365 | 3.876 | -2.961 | 5.14e-03 | 6.30e-02 | -2.274 | Plasmodium exported protein, unknown function | NA |
| 56 | PF3D7_0400700 | Pf3D7_04_v3 | 63104 | - | 1373 | -2.029 | -2.511 | -1.546 | -0.462 | -2.964 | 5.14e-03 | 6.30e-02 | -2.134 | rifin | RIF |
| 243 | PF3D7_0906000 | Pf3D7_09_v3 | 298665 | - | 5515 | -0.750 | -3.134 | 1.634 | 3.414 | -2.957 | 5.17e-03 | 6.30e-02 | -2.237 | exoribonuclease II | RNaseII |
| 487 | PF3D7_1361200 | Pf3D7_13_v3 | 2455261 | + | 6164 | -0.369 | -0.685 | -0.052 | 7.951 | -2.958 | 5.16e-03 | 6.30e-02 | -2.561 | conserved Plasmodium protein, unknown function | NA |
| 135 | PF3D7_0604500 | Pf3D7_06_v3 | 189012 | + | 9067 | -0.561 | -0.890 | -0.232 | 11.003 | -2.954 | 5.21e-03 | 6.30e-02 | -2.609 | conserved Plasmodium protein, unknown function | NA |
| 237 | PF3D7_0833500 | Pf3D7_08_v3 | 1435794 | - | 7656 | -0.964 | -1.526 | -0.403 | 4.351 | -2.953 | 5.22e-03 | 6.30e-02 | -2.271 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 465 | PF3D7_1341100 | Pf3D7_13_v3 | 1632602 | - | 108 | -1.057 | -1.456 | -0.659 | 3.016 | -2.954 | 5.21e-03 | 6.30e-02 | -2.180 | U6 spliceosomal RNA | NA |
| 202 | PF3D7_0803100 | Pf3D7_08_v3 | 199181 | - | 3738 | -0.554 | -1.417 | 0.308 | 8.102 | -2.951 | 5.25e-03 | 6.33e-02 | -2.579 | U3 small nucleolar RNA-associated protein 14, putative | UTP14 |
| 534 | PF3D7_1429100 | Pf3D7_14_v3 | 1142154 | + | 1638 | -1.087 | -1.692 | -0.483 | 3.402 | -2.951 | 5.28e-03 | 6.34e-02 | -2.243 | apicoplast ribosomal protein L15 precursor, putative | NA |
| 439 | PF3D7_1306400 | Pf3D7_13_v3 | 297178 | - | 1182 | -0.451 | -1.251 | 0.349 | 7.284 | -2.944 | 5.34e-03 | 6.40e-02 | -2.551 | 26S protease regulatory subunit 10B, putative | RPT4 |
| 293 | PF3D7_1016300 | Pf3D7_10_v3 | 650898 | - | 2670 | -0.743 | -1.261 | -0.225 | 6.278 | -2.944 | 5.36e-03 | 6.41e-02 | -2.469 | glycophorin binding protein | GBP |
| 144 | PF3D7_0613700 | Pf3D7_06_v3 | 559349 | - | 2112 | -0.721 | -2.430 | 0.989 | 3.628 | -2.938 | 5.44e-03 | 6.42e-02 | -2.315 | syntaxin binding protein, putative | NA |
| 206 | PF3D7_0806600 | Pf3D7_08_v3 | 349317 | - | 4046 | 0.530 | 0.151 | 0.909 | 5.537 | 2.938 | 5.43e-03 | 6.42e-02 | -2.423 | kinesin-like protein, putative | NA |
| 280 | PF3D7_1005000 | Pf3D7_10_v3 | 225456 | - | 2250 | 0.737 | -0.212 | 1.687 | 3.581 | 2.941 | 5.39e-03 | 6.42e-02 | -2.246 | methionine–tRNA ligase, putative | MRSapi |
| 296 | PF3D7_1018500 | Pf3D7_10_v3 | 735921 | - | 893 | -0.528 | -0.865 | -0.192 | 6.598 | -2.939 | 5.41e-03 | 6.42e-02 | -2.513 | PHF5-like protein, putative | NA |
| 428 | PF3D7_1252300 | Pf3D7_12_v3 | 2128400 | - | 387 | -0.756 | -1.518 | 0.005 | 8.882 | -2.943 | 5.46e-03 | 6.43e-02 | -2.618 | conserved Plasmodium protein, unknown function | NA |
| 61 | PF3D7_0404800 | Pf3D7_04_v3 | 264305 | - | 1866 | 1.425 | 0.637 | 2.212 | 2.020 | 2.938 | 5.48e-03 | 6.43e-02 | -2.192 | conserved Plasmodium protein, unknown function | NA |
| 244 | PF3D7_0906600 | Pf3D7_09_v3 | 320811 | - | 2532 | 0.483 | -1.418 | 2.384 | 9.190 | 2.932 | 5.53e-03 | 6.45e-02 | -2.654 | zinc finger protein, putative | NA |
| 345 | PF3D7_1126500 | Pf3D7_11_v3 | 1033062 | + | 4107 | 0.573 | -0.030 | 1.176 | 7.197 | 2.932 | 5.53e-03 | 6.45e-02 | -2.581 | conserved Plasmodium protein, unknown function | NA |
| 274 | PF3D7_1001000 | Pf3D7_10_v3 | 63152 | + | 881 | -0.979 | -1.809 | -0.149 | 3.798 | -2.933 | 5.54e-03 | 6.45e-02 | -2.352 | Plasmodium exported protein (hyp12), unknown function | PfJ13 |
| 335 | PF3D7_1120500 | Pf3D7_11_v3 | 772539 | + | 2504 | 0.414 | -0.202 | 1.031 | 6.939 | 2.929 | 5.56e-03 | 6.45e-02 | -2.566 | tRNA nucleotidyltransferase, putative | NA |
| 399 | PF3D7_1230900 | Pf3D7_12_v3 | 1267368 | + | 2814 | -0.432 | -1.171 | 0.308 | 9.390 | -2.928 | 5.59e-03 | 6.47e-02 | -2.663 | serine/threonine protein kinase RIO1, putative | RIO1 |
| 540 | PF3D7_1436900 | Pf3D7_14_v3 | 1500128 | - | 838 | 0.668 | 0.130 | 1.206 | 4.280 | 2.925 | 5.62e-03 | 6.49e-02 | -2.341 | histidine triad protein, putative | NA |
| 424 | PF3D7_1250000 | Pf3D7_12_v3 | 2044120 | + | 507 | -0.587 | -1.566 | 0.391 | 6.656 | -2.924 | 5.64e-03 | 6.50e-02 | -2.555 | rRNA-processing protein, putative | NA |
| 239 | PF3D7_0903100 | Pf3D7_09_v3 | 130140 | - | 798 | 0.680 | 0.256 | 1.104 | 4.674 | 2.919 | 5.71e-03 | 6.55e-02 | -2.385 | protein RER1, putative | RER1 |
| 26 | PF3D7_0218800 | Pf3D7_02_v3 | 766390 | - | 626 | 0.712 | 0.350 | 1.075 | 4.392 | 2.917 | 5.74e-03 | 6.56e-02 | -2.359 | ribonuclease P | NA |
| 503 | PF3D7_1402900 | Pf3D7_14_v3 | 106370 | + | 2865 | 1.270 | 0.847 | 1.693 | -0.495 | 2.916 | 5.76e-03 | 6.56e-02 | -2.222 | conserved Plasmodium protein, unknown function | NA |
| 545 | PF3D7_1441000 | Pf3D7_14_v3 | 1669980 | - | 1671 | 0.659 | 0.347 | 0.971 | 4.042 | 2.916 | 5.76e-03 | 6.56e-02 | -2.345 | cytoplasmic tRNA 2-thiolation protein 2, putative | NCS2 |
| 294 | PF3D7_1018000 | Pf3D7_10_v3 | 718454 | + | 1683 | 1.168 | 0.545 | 1.790 | 2.241 | 2.914 | 5.79e-03 | 6.57e-02 | -2.248 | tRNA pseudouridine synthase, putative | NA |
| 91 | PF3D7_0507600 | Pf3D7_05_v3 | 313199 | + | 1959 | 0.587 | -0.307 | 1.481 | 6.557 | 2.912 | 5.83e-03 | 6.58e-02 | -2.581 | cell differentiation protein, putative | CAF40 |
| 155 | PF3D7_0625600 | Pf3D7_06_v3 | 1039655 | + | 1896 | 0.874 | 0.463 | 1.284 | 5.591 | 2.914 | 5.85e-03 | 6.58e-02 | -2.489 | poly(A) polymerase PAP, putative | NA |
| 216 | PF3D7_0817200 | Pf3D7_08_v3 | 777257 | - | 2391 | 0.463 | 0.175 | 0.751 | 5.996 | 2.911 | 5.84e-03 | 6.58e-02 | -2.529 | conserved Plasmodium protein, unknown function | NA |
| 309 | PF3D7_1033200 | Pf3D7_10_v3 | 1335222 | + | 1068 | -0.713 | -0.952 | -0.474 | 7.027 | -2.911 | 5.86e-03 | 6.58e-02 | -2.581 | early transcribed membrane protein 10.2 | ETRAMP10.2 |
| 58 | PF3D7_0403700 | Pf3D7_04_v3 | 206228 | - | 3167 | -0.318 | -0.856 | 0.219 | 8.454 | -2.904 | 5.95e-03 | 6.65e-02 | -2.708 | pre-mRNA-splicing factor CLF1, putative | CLF1 |
| 203 | PF3D7_0803200 | Pf3D7_08_v3 | 204241 | - | 2421 | -1.030 | -2.425 | 0.365 | 1.745 | -2.902 | 5.97e-03 | 6.65e-02 | -2.261 | filament assembling protein, putative | NA |
| 514 | PF3D7_1412700 | Pf3D7_14_v3 | 512363 | + | 3660 | -0.526 | -1.135 | 0.083 | 5.946 | -2.903 | 5.96e-03 | 6.65e-02 | -2.550 | AAA family ATPase, putative | NA |
| 148 | PF3D7_0618200 | Pf3D7_06_v3 | 764667 | - | 826 | -0.492 | -0.787 | -0.197 | 7.053 | -2.898 | 6.04e-03 | 6.65e-02 | -2.656 | conserved Plasmodium protein, unknown function | NA |
| 193 | PF3D7_0723400 | Pf3D7_07_v3 | 978920 | - | 4269 | -0.411 | -1.124 | 0.303 | 9.715 | -2.898 | 6.03e-03 | 6.65e-02 | -2.742 | conserved Plasmodium protein, unknown function | NA |
| 288 | PF3D7_1015500 | Pf3D7_10_v3 | 624048 | - | 1848 | 0.912 | 0.030 | 1.794 | 0.006 | 2.899 | 6.03e-03 | 6.65e-02 | -2.255 | conserved Plasmodium protein, unknown function | NA |
| 497 | PF3D7_1368600 | Pf3D7_13_v3 | 2725669 | - | 279 | -0.901 | -1.216 | -0.586 | 2.009 | -2.896 | 6.07e-03 | 6.65e-02 | -2.284 | mitochondrial import inner membrane translocase subunit TIM9, putative | TIM9 |
| 522 | PF3D7_1417600 | Pf3D7_14_v3 | 730694 | - | 13989 | -0.453 | -1.308 | 0.401 | 8.923 | -2.897 | 6.05e-03 | 6.65e-02 | -2.734 | conserved Plasmodium protein, unknown function | NA |
| 535 | PF3D7_1432900 | Pf3D7_14_v3 | 1296173 | - | 1039 | 0.681 | 0.409 | 0.953 | 3.904 | 2.895 | 6.08e-03 | 6.65e-02 | -2.374 | SF-assemblin, putative | NA |
| 571 | PF3D7_1460200 | Pf3D7_14_v3 | 2456879 | - | 924 | 1.252 | 0.379 | 2.125 | 1.138 | 2.895 | 6.08e-03 | 6.65e-02 | -2.266 | conserved Plasmodium protein, unknown function | NA |
| 69 | PF3D7_0412900 | Pf3D7_04_v3 | 576810 | - | 7859 | -1.033 | -1.344 | -0.722 | 2.642 | -2.894 | 6.10e-03 | 6.65e-02 | -2.305 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 49 | PF3D7_0319600 | Pf3D7_03_v3 | 817913 | + | 783 | -0.419 | -0.965 | 0.128 | 8.342 | -2.891 | 6.15e-03 | 6.67e-02 | -2.737 | elongation factor 1 (EF-1), putative | NA |
| 444 | PF3D7_1309400 | Pf3D7_13_v3 | 431892 | + | 3984 | -0.653 | -1.269 | -0.037 | 5.709 | -2.891 | 6.14e-03 | 6.67e-02 | -2.550 | HORMA domain protein, putative | NA |
| 395 | PF3D7_1227800 | Pf3D7_12_v3 | 1134370 | - | 3279 | -0.355 | -0.694 | -0.017 | 9.186 | -2.890 | 6.17e-03 | 6.67e-02 | -2.755 | histone S-adenosyl methyltransferase, putative | NA |
| 538 | PF3D7_1436000 | Pf3D7_14_v3 | 1458131 | + | 1740 | -0.526 | -1.586 | 0.533 | 8.085 | -2.885 | 6.25e-03 | 6.74e-02 | -2.702 | glucose-6-phosphate isomerase | GPI |
| 520 | PF3D7_1416300 | Pf3D7_14_v3 | 659539 | + | 1365 | 0.945 | 0.145 | 1.745 | 1.326 | 2.884 | 6.27e-03 | 6.75e-02 | -2.294 | conserved protein, unknown function | NA |
| 71 | PF3D7_0416000 | Pf3D7_04_v3 | 701526 | - | 2637 | -0.645 | -1.233 | -0.058 | 6.301 | -2.883 | 6.29e-03 | 6.75e-02 | -2.630 | RNA-binding protein, putative | NA |
| 75 | PF3D7_0417800 | Pf3D7_04_v3 | 787243 | - | 2100 | -0.976 | -1.845 | -0.107 | 3.420 | -2.879 | 6.36e-03 | 6.81e-02 | -2.434 | cdc2-related protein kinase 1 | CRK1 |
| 117 | PF3D7_0523300 | Pf3D7_05_v3 | 970266 | - | 697 | 0.927 | 0.217 | 1.636 | 0.675 | 2.877 | 6.38e-03 | 6.81e-02 | -2.301 | conserved Plasmodium protein, unknown function | NA |
| 250 | PF3D7_0913200 | Pf3D7_09_v3 | 575679 | + | 831 | -0.479 | -1.061 | 0.103 | 8.889 | -2.869 | 6.51e-03 | 6.92e-02 | -2.802 | elongation factor 1-beta | EF-1beta |
| 407 | PF3D7_1240600 | Pf3D7_12_v3 | 1719574 | + | 7883 | -1.239 | -1.568 | -0.911 | 3.783 | -2.876 | 6.51e-03 | 6.92e-02 | -2.421 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 113 | PF3D7_0521800 | Pf3D7_05_v3 | 885714 | + | 2519 | 0.974 | 0.248 | 1.700 | 1.517 | 2.865 | 6.58e-03 | 6.95e-02 | -2.337 | nucleotide binding protein, putative | NA |
| 573 | PF3D7_1461600 | Pf3D7_14_v3 | 2498047 | - | 2338 | -0.535 | -2.218 | 1.149 | 8.956 | -2.866 | 6.57e-03 | 6.95e-02 | -2.809 | splicing factor 3B subunit 2, putative | SF3B2 |
| 87 | PF3D7_0502400 | Pf3D7_05_v3 | 109898 | - | 1794 | 0.704 | 0.466 | 0.942 | 7.883 | 2.865 | 6.65e-03 | 6.99e-02 | -2.776 | merozoite surface protein 8 | MSP8 |
| 354 | PF3D7_1137100 | Pf3D7_11_v3 | 1462168 | + | 903 | 0.544 | -0.168 | 1.256 | 5.368 | 2.861 | 6.65e-03 | 6.99e-02 | -2.586 | mitochondrial ribosomal protein S9 precursor, putative | NA |
| 371 | PF3D7_1206200 | Pf3D7_12_v3 | 275744 | - | 3593 | -0.499 | -0.804 | -0.193 | 10.135 | -2.859 | 6.70e-03 | 7.02e-02 | -2.840 | eukaryotic translation initiation factor 3 subunit C, putative | EIF3C |
| 34 | PF3D7_0303400 | Pf3D7_03_v3 | 178420 | + | 2708 | 0.968 | 0.445 | 1.490 | 1.373 | 2.854 | 6.77e-03 | 7.03e-02 | -2.358 | palmitoyltransferase DHHC1 | DHHC1 |
| 109 | PF3D7_0519400 | Pf3D7_05_v3 | 798036 | - | 740 | -0.466 | -0.773 | -0.159 | 9.741 | -2.857 | 6.72e-03 | 7.03e-02 | -2.841 | 40S ribosomal protein S24 | RPS24 |
| 360 | PF3D7_1143800 | Pf3D7_11_v3 | 1748439 | + | 2700 | 0.520 | 0.161 | 0.880 | 6.960 | 2.853 | 6.80e-03 | 7.03e-02 | -2.750 | conserved Plasmodium protein, unknown function | NA |
| 367 | PF3D7_1202900 | Pf3D7_12_v3 | 162429 | - | 294 | -0.574 | -0.891 | -0.258 | 9.229 | -2.853 | 6.80e-03 | 7.03e-02 | -2.846 | high mobility group protein B1 | HMGB1 |
| 468 | PF3D7_1344900 | Pf3D7_13_v3 | 1801271 | + | 4467 | 0.419 | 0.090 | 0.749 | 8.107 | 2.855 | 6.76e-03 | 7.03e-02 | -2.808 | conserved Plasmodium protein, unknown function | NA |
| 570 | PF3D7_1459300 | Pf3D7_14_v3 | 2432177 | + | 570 | 0.745 | 0.128 | 1.362 | 1.769 | 2.856 | 6.75e-03 | 7.03e-02 | -2.369 | OPA3-like protein, putative | NA |
| 124 | PF3D7_0527500 | Pf3D7_05_v3 | 1143618 | + | 1742 | -0.358 | -0.736 | 0.019 | 9.602 | -2.850 | 6.84e-03 | 7.05e-02 | -2.855 | Hsc70-interacting protein | HIP |
| 483 | PF3D7_1358700 | Pf3D7_13_v3 | 2326394 | - | 462 | 0.759 | 0.391 | 1.127 | 5.919 | 2.851 | 6.85e-03 | 7.05e-02 | -2.671 | YOP1-like protein, putative | YOP1L |
| 116 | PF3D7_0523200 | Pf3D7_05_v3 | 966123 | + | 3615 | 0.968 | 0.440 | 1.495 | 1.317 | 2.846 | 6.91e-03 | 7.06e-02 | -2.376 | conserved Plasmodium protein, unknown function | NA |
| 270 | PF3D7_0935600 | Pf3D7_09_v3 | 1405192 | + | 1831 | -1.141 | -1.561 | -0.720 | 9.813 | -2.868 | 6.92e-03 | 7.06e-02 | -2.811 | gametocytogenesis-implicated protein | GIG |
| 397 | PF3D7_1229600 | Pf3D7_12_v3 | 1214043 | - | 3673 | -0.941 | -1.789 | -0.094 | 1.439 | -2.844 | 6.95e-03 | 7.06e-02 | -2.381 | conserved Plasmodium protein, unknown function | NA |
| 486 | PF3D7_1361000 | Pf3D7_13_v3 | 2445090 | - | 2175 | 0.820 | -0.143 | 1.783 | 4.682 | 2.843 | 6.97e-03 | 7.06e-02 | -2.561 | protein arginine N-methyltransferase 5, putative | PRMT5 |
| 491 | PF3D7_1365000 | Pf3D7_13_v3 | 2608698 | + | 1047 | -0.778 | -1.316 | -0.241 | 3.911 | -2.844 | 6.95e-03 | 7.06e-02 | -2.483 | conserved Plasmodium protein, unknown function | NA |
| 576 | PF3D7_1467300 | Pf3D7_14_v3 | 2750958 | + | 1467 | 0.888 | 0.495 | 1.281 | 2.920 | 2.843 | 6.97e-03 | 7.06e-02 | -2.431 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | DXR |
| 33 | PF3D7_0303200 | Pf3D7_03_v3 | 169571 | + | 4730 | -0.698 | -1.308 | -0.088 | 3.533 | -2.836 | 7.10e-03 | 7.07e-02 | -2.512 | HAD superfamily protein, putative | NA |
| 104 | PF3D7_0517200 | Pf3D7_05_v3 | 720743 | - | 1899 | 0.627 | 0.255 | 1.000 | 7.316 | 2.838 | 7.07e-03 | 7.07e-02 | -2.802 | conserved Plasmodium protein, unknown function | NA |
| 228 | PF3D7_0826900 | Pf3D7_08_v3 | 1164655 | + | 2551 | 0.978 | -0.074 | 2.030 | 3.039 | 2.838 | 7.07e-03 | 7.07e-02 | -2.447 | conserved Plasmodium protein, unknown function | NA |
| 386 | PF3D7_1217400 | Pf3D7_12_v3 | 686307 | - | 2565 | 0.869 | 0.526 | 1.211 | 5.197 | 2.838 | 7.10e-03 | 7.07e-02 | -2.622 | conserved Plasmodium protein, unknown function | NA |
| 519 | PF3D7_1415600 | Pf3D7_14_v3 | 629419 | - | 3477 | -0.575 | -0.904 | -0.246 | 4.156 | -2.838 | 7.06e-03 | 7.07e-02 | -2.565 | conserved Plasmodium protein, unknown function | NA |
| 546 | PF3D7_1443300 | Pf3D7_14_v3 | 1776010 | + | 653 | -0.453 | -0.885 | -0.022 | 6.719 | -2.838 | 7.06e-03 | 7.07e-02 | -2.770 | U6 snRNA-associated Sm-like protein LSm5, putative | LSM5 |
| 562 | PF3D7_1452100 | Pf3D7_14_v3 | 2141662 | + | 1017 | 0.904 | 0.547 | 1.261 | 2.378 | 2.839 | 7.05e-03 | 7.07e-02 | -2.423 | leucine-rich repeat protein | LRR3 |
| 515 | PF3D7_1413800 | Pf3D7_14_v3 | 547954 | + | 1464 | 0.339 | -0.386 | 1.064 | 6.476 | 2.828 | 7.26e-03 | 7.21e-02 | -2.774 | diphthamide biosynthesis protein 1, putative | DPH1 |
| 57 | PF3D7_0403600 | Pf3D7_04_v3 | 197846 | - | 3363 | -1.163 | -1.574 | -0.753 | 2.273 | -2.828 | 7.28e-03 | 7.21e-02 | -2.467 | conserved Plasmodium protein, unknown function | NA |
| 23 | PF3D7_0211800 | Pf3D7_02_v3 | 475242 | + | 1833 | -0.587 | -1.433 | 0.260 | 9.276 | -2.823 | 7.37e-03 | 7.28e-02 | -2.916 | asparagine–tRNA ligase | AsnRS |
| 121 | PF3D7_0524500 | Pf3D7_05_v3 | 1016198 | + | 372 | 1.006 | 0.247 | 1.764 | 2.180 | 2.819 | 7.43e-03 | 7.28e-02 | -2.457 | conserved Plasmodium protein, unknown function | NA |
| 123 | PF3D7_0527300 | Pf3D7_05_v3 | 1135976 | - | 1895 | 0.530 | 0.138 | 0.922 | 6.450 | 2.815 | 7.51e-03 | 7.28e-02 | -2.797 | methionine aminopeptidase 1a, putative | METAP1a |
| 157 | PF3D7_0626800 | Pf3D7_06_v3 | 1078995 | + | 2326 | -0.591 | -1.198 | 0.017 | 11.922 | -2.818 | 7.48e-03 | 7.28e-02 | -2.932 | pyruvate kinase | PyrK |
| 218 | PF3D7_0819100 | Pf3D7_08_v3 | 869562 | + | 1013 | 0.442 | -0.140 | 1.024 | 5.546 | 2.820 | 7.41e-03 | 7.28e-02 | -2.702 | BRIX domain, putative | NA |
| 241 | PF3D7_0905200 | Pf3D7_09_v3 | 245261 | - | 3600 | 0.460 | -0.410 | 1.331 | 6.224 | 2.815 | 7.50e-03 | 7.28e-02 | -2.779 | mitochondrial carrier protein, putative | NA |
| 524 | PF3D7_1419000 | Pf3D7_14_v3 | 786958 | - | 3501 | 0.773 | -0.008 | 1.555 | 3.397 | 2.819 | 7.43e-03 | 7.28e-02 | -2.510 | conserved Plasmodium protein, unknown function | NA |
| 579 | PF3D7_1469900 | Pf3D7_14_v3 | 2866358 | + | 1826 | -1.223 | -1.484 | -0.963 | 0.011 | -2.816 | 7.49e-03 | 7.28e-02 | -2.427 | conserved Plasmodium protein, unknown function | NA |
| 581 | PF3D7_1472000 | Pf3D7_14_v3 | 2940478 | + | 1126 | -0.532 | -1.067 | 0.002 | 5.896 | -2.816 | 7.48e-03 | 7.28e-02 | -2.737 | pre-mRNA-splicing factor ISY1, putative | ISY1 |
| 17 | PF3D7_0202500 | Pf3D7_02_v3 | 127994 | + | 321 | -0.625 | -1.245 | -0.005 | 12.135 | -2.813 | 7.60e-03 | 7.33e-02 | -2.942 | early transcribed membrane protein 2 | ETRAMP2 |
| 473 | PF3D7_1347500 | Pf3D7_13_v3 | 1897983 | - | 1380 | -0.435 | -1.098 | 0.228 | 12.066 | -2.811 | 7.59e-03 | 7.33e-02 | -2.945 | DNA/RNA-binding protein Alba 4 | ALBA4 |
| 569 | PF3D7_1459100 | Pf3D7_14_v3 | 2423907 | + | 2394 | 1.078 | 0.676 | 1.480 | 1.903 | 2.810 | 7.60e-03 | 7.33e-02 | -2.466 | GTP-binding protein, putative | NA |
| 409 | PF3D7_1242900 | Pf3D7_12_v3 | 1808878 | - | 745 | 0.885 | 0.532 | 1.238 | 0.857 | 2.809 | 7.62e-03 | 7.33e-02 | -2.450 | mitochondrial import inner membrane translocase subunit TIM13, putative | TIM13 |
| 278 | PF3D7_1004100 | Pf3D7_10_v3 | 182244 | + | 4857 | 1.182 | 0.860 | 1.504 | 3.140 | 2.806 | 7.73e-03 | 7.41e-02 | -2.534 | hypothetical protein | NA |
| 548 | PF3D7_1445300 | Pf3D7_14_v3 | 1860148 | + | 1948 | 0.760 | 0.075 | 1.446 | 3.421 | 2.802 | 7.75e-03 | 7.42e-02 | -2.546 | mitochondrial ribosomal protein S29 precursor, putative | NA |
| 138 | PF3D7_0606900 | Pf3D7_06_v3 | 290426 | - | 660 | 0.980 | -0.161 | 2.121 | 3.885 | 2.802 | 7.78e-03 | 7.43e-02 | -2.596 | glutaredoxin-like protein | GLP2 |
| 142 | PF3D7_0612800 | Pf3D7_06_v3 | 528060 | - | 1116 | 0.778 | -0.966 | 2.523 | 3.897 | 2.798 | 7.84e-03 | 7.47e-02 | -2.595 | 6-cysteine protein | P12p |
| 406 | PF3D7_1240400 | Pf3D7_12_v3 | 1704512 | + | 7979 | -0.896 | -1.428 | -0.364 | 4.878 | -2.798 | 7.88e-03 | 7.49e-02 | -2.682 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 80 | PF3D7_0421300 | Pf3D7_04_v3 | 969031 | - | 7561 | -1.049 | -1.816 | -0.283 | 4.771 | -2.800 | 7.92e-03 | 7.51e-02 | -2.673 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 24 | PF3D7_0216400 | Pf3D7_02_v3 | 675431 | + | 2169 | 0.686 | 0.320 | 1.052 | 0.562 | 2.787 | 8.05e-03 | 7.61e-02 | -2.488 | vacuolar protein sorting-associated protein 45, putative | VPS45 |
| 377 | PF3D7_1211200 | Pf3D7_12_v3 | 491893 | - | 5496 | -0.455 | -0.978 | 0.069 | 7.015 | -2.787 | 8.07e-03 | 7.61e-02 | -2.905 | conserved Plasmodium protein, unknown function | NA |
| 498 | PF3D7_1370300 | Pf3D7_13_v3 | 2787972 | + | 942 | -0.743 | -1.526 | 0.041 | 11.370 | -2.794 | 8.09e-03 | 7.62e-02 | -3.001 | membrane associated histidine-rich protein | MAHRP1 |
| 245 | PF3D7_0907400 | Pf3D7_09_v3 | 351955 | - | 2769 | -0.479 | -1.407 | 0.449 | 8.348 | -2.784 | 8.13e-03 | 7.64e-02 | -2.973 | ATP-dependent protease ATPase subunit ClpY | ClpY |
| 530 | PF3D7_1426100 | Pf3D7_14_v3 | 1018745 | - | 516 | 0.385 | -0.100 | 0.869 | 7.977 | 2.783 | 8.15e-03 | 7.64e-02 | -2.974 | basic transcription factor 3b, putative | NA |
| 223 | PF3D7_0822300 | Pf3D7_08_v3 | 988281 | - | 483 | 0.532 | 0.128 | 0.937 | 4.939 | 2.781 | 8.18e-03 | 7.65e-02 | -2.726 | small nuclear ribonucleoprotein G, putative | SNRPG |
| 195 | PF3D7_0724000 | Pf3D7_07_v3 | 1006335 | + | 5811 | 0.840 | 0.470 | 1.211 | 2.272 | 2.779 | 8.22e-03 | 7.67e-02 | -2.545 | Rab GTPase activator and protein kinase, putative | NA |
| 261 | PF3D7_0924600 | Pf3D7_09_v3 | 999463 | + | 6383 | -1.220 | -1.505 | -0.935 | 0.790 | -2.777 | 8.26e-03 | 7.70e-02 | -2.515 | conserved Plasmodium protein, unknown function | NA |
| 149 | PF3D7_0621300 | Pf3D7_06_v3 | 873809 | + | 2382 | 0.383 | -0.299 | 1.064 | 7.567 | 2.776 | 8.31e-03 | 7.70e-02 | -2.972 | mRNA binding Pumilio-homology domain protein, putative | NA |
| 508 | PF3D7_1406200 | Pf3D7_14_v3 | 217845 | + | 8463 | -0.453 | -1.583 | 0.677 | 9.513 | -2.775 | 8.31e-03 | 7.70e-02 | -3.031 | conserved Plasmodium protein, unknown function | NA |
| 574 | PF3D7_1462800 | Pf3D7_14_v3 | 2559098 | + | 1250 | -0.626 | -1.385 | 0.132 | 13.115 | -2.776 | 8.34e-03 | 7.72e-02 | -3.015 | glyceraldehyde-3-phosphate dehydrogenase | GAPDH |
| 306 | PF3D7_1027500 | Pf3D7_10_v3 | 1147866 | + | 348 | 0.923 | 0.672 | 1.174 | 0.639 | 2.771 | 8.40e-03 | 7.75e-02 | -2.524 | conserved Plasmodium protein, unknown function | NA |
| 35 | PF3D7_0304300 | Pf3D7_03_v3 | 212283 | + | 4290 | 1.106 | 0.823 | 1.389 | 1.180 | 2.768 | 8.46e-03 | 7.76e-02 | -2.537 | conserved Plasmodium protein, unknown function | NA |
| 73 | PF3D7_0416200 | Pf3D7_04_v3 | 709460 | - | 624 | -1.454 | -1.984 | -0.924 | 2.998 | -2.777 | 8.43e-03 | 7.76e-02 | -2.582 | conserved protein, unknown function | NA |
| 174 | PF3D7_0708900 | Pf3D7_07_v3 | 399290 | - | 954 | 0.770 | 0.472 | 1.068 | 4.297 | 2.767 | 8.48e-03 | 7.76e-02 | -2.704 | Cg3 protein | NA |
| 502 | PF3D7_1402300 | Pf3D7_14_v3 | 85883 | - | 2001 | 0.445 | 0.077 | 0.813 | 6.935 | 2.768 | 8.48e-03 | 7.76e-02 | -2.955 | 26S proteasome regulatory subunit RPN6 | RPN6 |
| 324 | PF3D7_1107800 | Pf3D7_11_v3 | 329867 | - | 5735 | -0.728 | -1.456 | 0.000 | 8.457 | -2.765 | 8.65e-03 | 7.89e-02 | -3.001 | transcription factor with AP2 domain(s) | ApiAP2 |
| 191 | PF3D7_0721700 | Pf3D7_07_v3 | 935497 | + | 1404 | 0.843 | 0.100 | 1.585 | 2.869 | 2.756 | 8.72e-03 | 7.95e-02 | -2.621 | secreted ookinete protein, putative | PSOP1 |
| 236 | PF3D7_0831750 | Pf3D7_08_v3 | 1371847 | + | 874 | 1.027 | 0.335 | 1.718 | 2.561 | 2.753 | 8.81e-03 | 7.95e-02 | -2.614 | Plasmodium exported protein (PHISTa), unknown function, pseudogene | NA |
| 315 | PF3D7_1102600 | Pf3D7_11_v3 | 123818 | - | 919 | 1.279 | 0.897 | 1.661 | 2.320 | 2.755 | 8.81e-03 | 7.95e-02 | -2.609 | Plasmodium exported protein, unknown function | GEXP14 |
| 459 | PF3D7_1332000 | Pf3D7_13_v3 | 1325913 | - | 1620 | 0.574 | 0.239 | 0.910 | 4.779 | 2.755 | 8.75e-03 | 7.95e-02 | -2.778 | syntaxin, Qa-SNARE family | SYN5 |
| 537 | PF3D7_1435400 | Pf3D7_14_v3 | 1433738 | - | 573 | 0.388 | -0.187 | 0.963 | 6.059 | 2.754 | 8.79e-03 | 7.95e-02 | -2.908 | ER membrane protein complex subunit 4, putative | EMC4 |
| 192 | PF3D7_0722300 | Pf3D7_07_v3 | 949449 | - | 3666 | 0.483 | 0.218 | 0.749 | 6.531 | 2.749 | 8.89e-03 | 8.01e-02 | -2.961 | ubiquitin carboxyl-terminal hydrolase, putative | NA |
| 40 | PF3D7_0311600 | Pf3D7_03_v3 | 499602 | + | 2752 | 1.038 | 0.746 | 1.331 | 2.539 | 2.744 | 9.00e-03 | 8.09e-02 | -2.635 | dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit 1, putative | NA |
| 101 | PF3D7_0516100 | Pf3D7_05_v3 | 667486 | + | 7376 | 0.809 | -0.170 | 1.787 | 3.482 | 2.740 | 9.09e-03 | 8.09e-02 | -2.688 | cation-transporting ATPase 1 | ATPase1 |
| 178 | PF3D7_0711700 | Pf3D7_07_v3 | 511950 | - | 7476 | -0.789 | -1.093 | -0.485 | 4.598 | -2.741 | 9.08e-03 | 8.09e-02 | -2.793 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 200 | PF3D7_0800900 | Pf3D7_08_v3 | 83128 | + | 777 | -1.118 | -1.653 | -0.582 | 3.284 | -2.743 | 9.15e-03 | 8.09e-02 | -2.745 | Plasmodium exported protein (hyp7), unknown function, pseudogene | NA |
| 211 | PF3D7_0812700 | Pf3D7_08_v3 | 633990 | + | 708 | 0.535 | -0.065 | 1.135 | 5.781 | 2.738 | 9.15e-03 | 8.09e-02 | -2.915 | RNA-binding protein (U1 snRNP-like), putative | NA |
| 227 | PF3D7_0826100 | Pf3D7_08_v3 | 1113369 | - | 25776 | -0.478 | -0.970 | 0.014 | 10.241 | -2.741 | 9.08e-03 | 8.09e-02 | -3.117 | E3 ubiquitin-protein ligase, putative | NA |
| 265 | PF3D7_0929200 | Pf3D7_09_v3 | 1167842 | + | 1736 | 0.364 | -0.669 | 1.398 | 8.361 | 2.740 | 9.10e-03 | 8.09e-02 | -3.087 | RNA-binding protein, putative | NA |
| 304 | PF3D7_1027100 | Pf3D7_10_v3 | 1133838 | - | 2319 | -0.441 | -1.158 | 0.276 | 8.266 | -2.736 | 9.18e-03 | 8.09e-02 | -3.094 | U3 small nucleolar ribonucleoprotein protein MPP10, putative | MPP10 |
| 327 | PF3D7_1109900 | Pf3D7_11_v3 | 397124 | + | 652 | -0.659 | -0.936 | -0.382 | 7.738 | -2.738 | 9.21e-03 | 8.09e-02 | -3.073 | 60S ribosomal protein L36 | RPL36 |
| 415 | PF3D7_1244900 | Pf3D7_12_v3 | 1877039 | + | 3003 | 0.762 | 0.196 | 1.328 | 0.883 | 2.738 | 9.15e-03 | 8.09e-02 | -2.595 | conserved Plasmodium protein, unknown function | NA |
| 457 | PF3D7_1330200 | Pf3D7_13_v3 | 1275104 | + | 796 | 0.723 | -0.257 | 1.704 | 2.434 | 2.743 | 9.03e-03 | 8.09e-02 | -2.627 | conserved Plasmodium protein, unknown function | NA |
| 558 | PF3D7_1450600 | Pf3D7_14_v3 | 2075586 | - | 1764 | 0.338 | -0.567 | 1.242 | 6.523 | 2.735 | 9.21e-03 | 8.09e-02 | -2.996 | S-adenosylmethionine-dependent methyltransferase, putative | NA |
| 422 | PF3D7_1248600 | Pf3D7_12_v3 | 1988237 | + | 2509 | 1.120 | 0.763 | 1.478 | 5.174 | 2.743 | 9.26e-03 | 8.12e-02 | -2.851 | conserved Plasmodium protein, unknown function | NA |
| 5 | PF3D7_0104200 | Pf3D7_01_v3 | 182822 | - | 1401 | 1.145 | -0.211 | 2.501 | 4.099 | 2.737 | 9.29e-03 | 8.13e-02 | -2.756 | StAR-related lipid transfer protein | NA |
| 229 | PF3D7_0827000 | Pf3D7_08_v3 | 1167579 | - | 3870 | -0.328 | -1.125 | 0.469 | 8.724 | -2.730 | 9.34e-03 | 8.13e-02 | -3.125 | ATP-dependent RNA helicase DBP10, putative | DBP10 |
| 414 | PF3D7_1244800 | Pf3D7_12_v3 | 1873194 | - | 2094 | -0.383 | -0.636 | -0.129 | 7.604 | -2.730 | 9.33e-03 | 8.13e-02 | -3.081 | cytoplasmic translation machinery associated protein, putative | NA |
| 105 | PF3D7_0517600 | Pf3D7_05_v3 | 740156 | - | 879 | 1.044 | 0.709 | 1.379 | 1.434 | 2.726 | 9.42e-03 | 8.18e-02 | -2.630 | F-actin-capping protein subunit beta, putative | CPbeta |
| 3 | PF3D7_0100100 | Pf3D7_01_v3 | 29510 | + | 7617 | -0.834 | -1.453 | -0.215 | 4.119 | -2.721 | 9.56e-03 | 8.20e-02 | -2.780 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 127 | PF3D7_0528600 | Pf3D7_05_v3 | 1176969 | - | 318 | -0.560 | -0.933 | -0.186 | 4.198 | -2.722 | 9.52e-03 | 8.20e-02 | -2.786 | conserved Plasmodium protein, unknown function | NA |
| 276 | PF3D7_1003700 | Pf3D7_10_v3 | 166743 | - | 3927 | 0.730 | 0.439 | 1.021 | 4.247 | 2.721 | 9.54e-03 | 8.20e-02 | -2.796 | conserved Plasmodium protein, unknown function | NA |
| 381 | PF3D7_1214600 | Pf3D7_12_v3 | 613561 | - | 1014 | -0.499 | -1.155 | 0.158 | 4.795 | -2.724 | 9.48e-03 | 8.20e-02 | -2.843 | adrenodoxin-type ferredoxin, putative | NA |
| 475 | PF3D7_1350100 | Pf3D7_13_v3 | 2005962 | - | 1989 | -0.397 | -0.739 | -0.055 | 9.200 | -2.721 | 9.56e-03 | 8.20e-02 | -3.156 | lysine–tRNA ligase | KRS1 |
| 510 | PF3D7_1409600 | Pf3D7_14_v3 | 374800 | + | 2307 | 0.745 | 0.012 | 1.478 | 5.160 | 2.723 | 9.51e-03 | 8.20e-02 | -2.879 | conserved Plasmodium protein, unknown function | NA |
| 65 | PF3D7_0406500 | Pf3D7_04_v3 | 334282 | - | 9773 | -1.156 | -1.624 | -0.688 | 10.276 | -2.734 | 9.76e-03 | 8.27e-02 | -3.156 | NYN domain-containing protein, putative | NA |
| 171 | PF3D7_0708000 | Pf3D7_07_v3 | 368707 | + | 2966 | 0.740 | 0.474 | 1.006 | 3.189 | 2.712 | 9.78e-03 | 8.27e-02 | -2.740 | cytoskeleton associated protein, putative | NA |
| 368 | PF3D7_1203700 | Pf3D7_12_v3 | 187146 | - | 1697 | -0.453 | -0.775 | -0.130 | 10.884 | -2.715 | 9.70e-03 | 8.27e-02 | -3.173 | nucleosome assembly protein | NAPL |
| 405 | PF3D7_1239800 | Pf3D7_12_v3 | 1660451 | + | 17304 | -0.912 | -1.490 | -0.334 | 3.750 | -2.715 | 9.71e-03 | 8.27e-02 | -2.792 | conserved Plasmodium protein, unknown function | NA |
| 426 | PF3D7_1251000 | Pf3D7_12_v3 | 2085370 | - | 1590 | 0.916 | 0.271 | 1.561 | 2.530 | 2.713 | 9.75e-03 | 8.27e-02 | -2.702 | conserved Plasmodium protein, unknown function | NA |
| 495 | PF3D7_1366700 | Pf3D7_13_v3 | 2666666 | + | 1116 | 1.060 | 0.474 | 1.645 | 1.359 | 2.714 | 9.72e-03 | 8.27e-02 | -2.655 | conserved Plasmodium protein, unknown function | NA |
| 583 | PF3D7_1473900 | Pf3D7_14_v3 | 3007601 | + | 2559 | 0.526 | -0.375 | 1.427 | 7.093 | 2.712 | 9.77e-03 | 8.27e-02 | -3.084 | conserved Plasmodium protein, unknown function | NA |
| 553 | PF3D7_1447100 | Pf3D7_14_v3 | 1932421 | - | 780 | -0.575 | -0.955 | -0.194 | 6.513 | -2.708 | 9.86e-03 | 8.32e-02 | -3.045 | conserved Plasmodium protein, unknown function | NA |
| 99 | PF3D7_0512800 | Pf3D7_05_v3 | 548406 | - | 4935 | -0.765 | -2.202 | 0.672 | 3.153 | -2.706 | 9.92e-03 | 8.35e-02 | -2.779 | conserved Plasmodium protein, unknown function | NA |
| 209 | PF3D7_0810800 | Pf3D7_08_v3 | 548200 | + | 2417 | -1.010 | -1.276 | -0.743 | 7.259 | -2.717 | 1.00e-02 | 8.35e-02 | -3.071 | hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase | PPPK-DHPS |
| 215 | PF3D7_0816600 | Pf3D7_08_v3 | 762118 | - | 3213 | -0.947 | -1.320 | -0.573 | 5.051 | -2.706 | 1.01e-02 | 8.35e-02 | -2.942 | chaperone protein ClpB1 | ClpB1 |
| 318 | PF3D7_1103000 | Pf3D7_11_v3 | 138646 | + | 389 | 0.964 | 0.556 | 1.372 | 1.515 | 2.702 | 1.00e-02 | 8.35e-02 | -2.683 | conserved Plasmodium protein, unknown function | NA |
| 334 | PF3D7_1120000 | Pf3D7_11_v3 | 756192 | + | 4244 | -0.613 | -1.493 | 0.268 | 7.431 | -2.706 | 9.97e-03 | 8.35e-02 | -3.128 | conserved Plasmodium protein, unknown function | NA |
| 344 | PF3D7_1126400 | Pf3D7_11_v3 | 1030679 | + | 803 | -0.398 | -1.015 | 0.219 | 5.816 | -2.704 | 9.98e-03 | 8.35e-02 | -2.994 | large ribosomal subunit processing factor, putative | NA |
| 416 | PF3D7_1246000 | Pf3D7_12_v3 | 1912457 | + | 2139 | 0.861 | 0.471 | 1.251 | 1.962 | 2.702 | 1.00e-02 | 8.35e-02 | -2.696 | conserved Plasmodium protein, unknown function | NA |
| 418 | PF3D7_1246700 | Pf3D7_12_v3 | 1938643 | + | 1323 | 0.928 | 0.133 | 1.724 | 1.236 | 2.700 | 1.01e-02 | 8.35e-02 | -2.682 | conserved Plasmodium protein, unknown function | NA |
| 460 | PF3D7_1332100 | Pf3D7_13_v3 | 1329491 | + | 1569 | 1.285 | 0.992 | 1.578 | -0.358 | 2.701 | 1.01e-02 | 8.35e-02 | -2.659 | conserved Plasmodium membrane protein, unknown function | NA |
| 152 | PF3D7_0623300 | Pf3D7_06_v3 | 947493 | - | 1152 | 1.080 | 0.385 | 1.776 | 1.961 | 2.698 | 1.01e-02 | 8.37e-02 | -2.707 | EGF-like membrane protein, putative | NA |
| 383 | PF3D7_1216400 | Pf3D7_12_v3 | 653670 | + | 2766 | 0.842 | 0.557 | 1.128 | 5.754 | 2.702 | 1.01e-02 | 8.37e-02 | -2.994 | conserved Plasmodium membrane protein, unknown function | NA |
| 186 | PF3D7_0717400 | Pf3D7_07_v3 | 751877 | + | 2256 | -0.371 | -0.623 | -0.118 | 7.670 | -2.695 | 1.02e-02 | 8.40e-02 | -3.161 | queuine tRNA-ribosyltransferase, putative | NA |
| 119 | PF3D7_0523900 | Pf3D7_05_v3 | 993433 | - | 1175 | 0.823 | -0.342 | 1.987 | 4.138 | 2.694 | 1.02e-02 | 8.41e-02 | -2.856 | conserved Plasmodium membrane protein, unknown function | NA |
| 474 | PF3D7_1349300 | Pf3D7_13_v3 | 1977269 | + | 5424 | 0.542 | -0.045 | 1.129 | 5.329 | 2.692 | 1.03e-02 | 8.42e-02 | -2.970 | tyrosine kinase-like protein | TKL3 |
| 563 | PF3D7_1452200 | Pf3D7_14_v3 | 2143302 | + | 1575 | 0.927 | 0.327 | 1.527 | 0.039 | 2.692 | 1.03e-02 | 8.42e-02 | -2.678 | aminomethyltransferase, putative | NA |
| 362 | PF3D7_1148600 | Pf3D7_11_v3 | 1925942 | + | 7209 | -3.035 | -3.785 | -2.285 | 4.294 | -2.718 | 1.03e-02 | 8.42e-02 | -2.821 | 18S ribosomal RNA | NA |
| 342 | PF3D7_1126100 | Pf3D7_11_v3 | 1018366 | - | 4130 | 0.859 | 0.471 | 1.246 | 1.624 | 2.688 | 1.04e-02 | 8.48e-02 | -2.719 | autophagy-related protein 7, putative | ATG7 |
| 67 | PF3D7_0412400 | Pf3D7_04_v3 | 545987 | - | 7824 | -0.809 | -0.997 | -0.621 | 3.478 | -2.685 | 1.05e-02 | 8.53e-02 | -2.805 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 82 | PF3D7_0424700 | Pf3D7_04_v3 | 1118430 | + | 3985 | -0.650 | -1.866 | 0.567 | 9.257 | -2.687 | 1.05e-02 | 8.55e-02 | -3.229 | serine/threonine protein kinase, FIKK family | FIKK4.2 |
| 509 | PF3D7_1408400 | Pf3D7_14_v3 | 313975 | - | 3483 | 0.583 | -0.068 | 1.235 | 4.984 | 2.681 | 1.06e-02 | 8.57e-02 | -2.967 | DNA repair helicase, putative | NA |
| 154 | PF3D7_0625400 | Pf3D7_06_v3 | 1032536 | - | 1239 | 0.471 | 0.212 | 0.729 | 7.757 | 2.679 | 1.06e-02 | 8.59e-02 | -3.200 | conserved Plasmodium protein, unknown function | NA |
| 286 | PF3D7_1013500 | Pf3D7_10_v3 | 526840 | + | 4609 | 0.790 | 0.184 | 1.396 | 5.066 | 2.679 | 1.06e-02 | 8.59e-02 | -2.975 | phosphoinositide-specific phospholipase C | PI-PLC |
| 421 | PF3D7_1248300 | Pf3D7_12_v3 | 1979786 | - | 414 | 1.076 | 0.633 | 1.518 | 1.684 | 2.678 | 1.06e-02 | 8.59e-02 | -2.739 | conserved Plasmodium membrane protein, unknown function | NA |
| 107 | PF3D7_0518400 | Pf3D7_05_v3 | 762103 | - | 690 | 1.074 | 0.336 | 1.813 | -0.117 | 2.674 | 1.08e-02 | 8.62e-02 | -2.712 | cyclin, putative | CYC3 |
| 214 | PF3D7_0815900 | Pf3D7_08_v3 | 743505 | + | 2001 | 0.951 | 0.490 | 1.411 | 0.836 | 2.675 | 1.07e-02 | 8.62e-02 | -2.722 | dihydrolipoyl dehydrogenase, apicoplast | aLipDH |
| 477 | PF3D7_1352500 | Pf3D7_13_v3 | 2093365 | - | 973 | -0.474 | -0.773 | -0.175 | 6.587 | -2.674 | 1.08e-02 | 8.62e-02 | -3.142 | thioredoxin-related protein, putative | NA |
| 212 | PF3D7_0812800 | Pf3D7_08_v3 | 635537 | - | 219 | 0.753 | 0.380 | 1.127 | 0.380 | 2.671 | 1.08e-02 | 8.65e-02 | -2.724 | conserved Plasmodium protein, unknown function | NA |
| 472 | PF3D7_1347300 | Pf3D7_13_v3 | 1893613 | - | 1411 | 0.784 | -0.066 | 1.634 | 1.989 | 2.672 | 1.08e-02 | 8.65e-02 | -2.762 | conserved Plasmodium membrane protein, unknown function | NA |
| 559 | PF3D7_1450700 | Pf3D7_14_v3 | 2078488 | + | 1863 | -0.496 | -0.943 | -0.049 | 7.376 | -2.669 | 1.09e-02 | 8.68e-02 | -3.202 | conserved Plasmodium protein, unknown function | NA |
| 64 | PF3D7_0405700 | Pf3D7_04_v3 | 305746 | - | 7248 | -0.675 | -1.452 | 0.101 | 3.443 | -2.667 | 1.10e-02 | 8.69e-02 | -2.913 | lysine decarboxylase, putative | NA |
| 253 | PF3D7_0915300 | Pf3D7_09_v3 | 646951 | - | 2166 | 0.725 | -0.216 | 1.666 | 3.428 | 2.668 | 1.09e-02 | 8.69e-02 | -2.845 | conserved Plasmodium protein, unknown function | NA |
| 330 | PF3D7_1111700 | Pf3D7_11_v3 | 452459 | - | 2403 | 0.581 | 0.082 | 1.080 | 3.957 | 2.663 | 1.11e-02 | 8.77e-02 | -2.901 | conserved Plasmodium protein, unknown function | NA |
| 575 | PF3D7_1466400 | Pf3D7_14_v3 | 2714844 | - | 2442 | 0.497 | -0.565 | 1.560 | 8.609 | 2.656 | 1.12e-02 | 8.89e-02 | -3.285 | transcription factor with AP2 domain(s) | ApiAP2 |
| 585 | PF3D7_1474700 | Pf3D7_14_v3 | 3063191 | - | 2573 | 0.855 | 0.507 | 1.203 | 2.302 | 2.656 | 1.13e-02 | 8.89e-02 | -2.817 | protein kinase, putative | NA |
| 419 | PF3D7_1247400 | Pf3D7_12_v3 | 1955124 | - | 915 | -0.542 | -0.882 | -0.202 | 6.290 | -2.654 | 1.13e-02 | 8.91e-02 | -3.159 | peptidyl-prolyl cis-trans isomerase FKBP35 | FKBP35 |
| 430 | PF3D7_1253200 | Pf3D7_12_v3 | 2173799 | - | 524 | -1.162 | -2.604 | 0.279 | -0.284 | -2.654 | 1.13e-02 | 8.91e-02 | -2.752 | hypothetical protein | NA |
| 301 | PF3D7_1023000 | Pf3D7_10_v3 | 961066 | - | 1242 | 0.753 | -0.184 | 1.690 | 1.353 | 2.652 | 1.14e-02 | 8.92e-02 | -2.784 | conserved Plasmodium membrane protein, unknown function | NA |
| 461 | PF3D7_1333400 | Pf3D7_13_v3 | 1370083 | + | 717 | 0.555 | 0.015 | 1.095 | 6.775 | 2.652 | 1.14e-02 | 8.92e-02 | -3.198 | conserved protein, unknown function | NA |
| 95 | PF3D7_0510500 | Pf3D7_05_v3 | 445983 | - | 2520 | -0.558 | -1.644 | 0.528 | 5.623 | -2.647 | 1.15e-02 | 9.00e-02 | -3.114 | topoisomerase I | TopoI |
| 230 | PF3D7_0827800 | Pf3D7_08_v3 | 1198858 | + | 7200 | -0.449 | -1.217 | 0.320 | 7.831 | -2.646 | 1.15e-02 | 9.01e-02 | -3.284 | SET domain protein, putative | SET3 |
| 256 | PF3D7_0918900 | Pf3D7_09_v3 | 777558 | + | 3192 | 0.467 | -0.229 | 1.163 | 7.837 | 2.645 | 1.16e-02 | 9.01e-02 | -3.282 | gamma-glutamylcysteine synthetase | gammaGCS |
| 146 | PF3D7_0615000 | Pf3D7_06_v3 | 622272 | + | 441 | -0.676 | -0.916 | -0.437 | 3.668 | -2.641 | 1.17e-02 | 9.03e-02 | -2.911 | conserved Plasmodium protein, unknown function | NA |
| 175 | PF3D7_0709200 | Pf3D7_07_v3 | 412343 | - | 819 | 0.795 | 0.496 | 1.095 | 1.276 | 2.641 | 1.17e-02 | 9.03e-02 | -2.805 | glutaredoxin-like protein | GLP3 |
| 527 | PF3D7_1423200 | Pf3D7_14_v3 | 933059 | + | 2299 | -0.492 | -1.236 | 0.253 | 5.923 | -2.641 | 1.17e-02 | 9.03e-02 | -3.154 | peptidyl-prolyl cis-trans isomerase | CYP52 |
| 543 | PF3D7_1439700 | Pf3D7_14_v3 | 1613853 | - | 1690 | 0.905 | 0.618 | 1.192 | 0.191 | 2.641 | 1.17e-02 | 9.03e-02 | -2.784 | leucine carboxyl methyltransferase, putative | NA |
| 556 | PF3D7_1450100 | Pf3D7_14_v3 | 2051621 | - | 1503 | 0.378 | -0.542 | 1.299 | 8.446 | 2.643 | 1.16e-02 | 9.03e-02 | -3.312 | signal recognition particle subunit SRP54 | SRP54 |
| 53 | PF3D7_0324800 | Pf3D7_03_v3 | 1027571 | + | 1359 | -1.666 | -2.748 | -0.584 | -0.333 | -2.640 | 1.18e-02 | 9.06e-02 | -2.780 | rifin | RIF |
| 387 | PF3D7_1218500 | Pf3D7_12_v3 | 725841 | - | 3997 | -0.424 | -0.723 | -0.126 | 9.347 | -2.639 | 1.18e-02 | 9.06e-02 | -3.335 | conserved Plasmodium protein, unknown function | NA |
| 505 | PF3D7_1404100 | Pf3D7_14_v3 | 145134 | - | 516 | -0.458 | -1.116 | 0.200 | 5.102 | -2.637 | 1.18e-02 | 9.06e-02 | -3.085 | cytochrome c, putative | NA |
| 199 | PF3D7_0800300 | Pf3D7_08_v3 | 40948 | + | 9992 | -0.816 | -1.213 | -0.419 | 5.113 | -2.638 | 1.18e-02 | 9.07e-02 | -3.066 | erythrocyte membrane protein 1, PfEMP1 | VAR |
| 190 | PF3D7_0721600 | Pf3D7_07_v3 | 931459 | - | 706 | -0.412 | -0.792 | -0.031 | 10.693 | -2.634 | 1.19e-02 | 9.09e-02 | -3.360 | 40S ribosomal protein S5, putative | NA |
| 523 | PF3D7_1417700 | Pf3D7_14_v3 | 750330 | + | 1355 | -0.499 | -0.893 | -0.105 | 4.889 | -2.633 | 1.19e-02 | 9.10e-02 | -3.061 | conserved Plasmodium protein, unknown function | NA |
| 153 | PF3D7_0624600 | Pf3D7_06_v3 | 999524 | + | 8160 | -0.447 | -0.713 | -0.182 | 10.780 | -2.632 | 1.20e-02 | 9.11e-02 | -3.365 | SNF2 helicase, putative | ISWI |
| 564 | PF3D7_1454300 | Pf3D7_14_v3 | 2229284 | + | 2298 | 0.979 | 0.656 | 1.302 | 2.334 | 2.631 | 1.20e-02 | 9.11e-02 | -2.866 | serine/threonine protein kinase KIN | KIN |
| 48 | PF3D7_0319500 | Pf3D7_03_v3 | 815569 | + | 1287 | -0.473 | -0.827 | -0.119 | 7.080 | -2.627 | 1.21e-02 | 9.17e-02 | -3.283 | RNA-binding protein, putative | NA |
| 339 | PF3D7_1122900 | Pf3D7_11_v3 | 878969 | + | 16305 | -0.879 | -1.148 | -0.609 | 1.460 | -2.627 | 1.21e-02 | 9.17e-02 | -2.849 | dynein heavy chain, putative | NA |
| 462 | PF3D7_1334200 | Pf3D7_13_v3 | 1398271 | + | 1575 | 0.506 | -0.050 | 1.063 | 6.071 | 2.627 | 1.21e-02 | 9.17e-02 | -3.195 | chaperone binding protein, putative | NA |
| 97 | PF3D7_0511500 | Pf3D7_05_v3 | 486602 | + | 30186 | -0.607 | -1.610 | 0.395 | 10.868 | -2.629 | 1.22e-02 | 9.17e-02 | -3.376 | RNA pseudouridylate synthase, putative | NA |
| 513 | PF3D7_1412100 | Pf3D7_14_v3 | 484438 | + | 2871 | 1.011 | 0.085 | 1.937 | 2.315 | 2.626 | 1.21e-02 | 9.17e-02 | -2.869 | conserved Plasmodium protein, unknown function | NA |
| 172 | PF3D7_0708400 | Pf3D7_07_v3 | 381592 | + | 3023 | -0.372 | -0.756 | 0.012 | 12.204 | -2.624 | 1.22e-02 | 9.17e-02 | -3.373 | heat shock protein 90 | HSP90 |
| 207 | PF3D7_0807600 | Pf3D7_08_v3 | 389596 | - | 4664 | -0.388 | -0.885 | 0.109 | 9.522 | -2.621 | 1.23e-02 | 9.22e-02 | -3.385 | conserved Plasmodium protein, unknown function | NA |
| 269 | PF3D7_0934500 | Pf3D7_09_v3 | 1350836 | - | 1094 | -0.372 | -0.695 | -0.048 | 6.863 | -2.618 | 1.24e-02 | 9.28e-02 | -3.286 | V-type proton ATPase subunit E, putative | NA |
| 369 | PF3D7_1205400 | Pf3D7_12_v3 | 232389 | - | 3258 | 1.011 | 0.447 | 1.576 | 3.919 | 2.617 | 1.25e-02 | 9.35e-02 | -3.007 | kelch domain-containing protein, putative | NA |
| 252 | PF3D7_0914700 | Pf3D7_09_v3 | 630657 | + | 1551 | 0.831 | -0.152 | 1.814 | 6.915 | 2.619 | 1.26e-02 | 9.38e-02 | -3.290 | major facilitator superfamily-related transporter, putative | MFR4 |
| 290 | PF3D7_1015800 | Pf3D7_10_v3 | 633682 | + | 1605 | 0.956 | 0.355 | 1.557 | 0.399 | 2.612 | 1.26e-02 | 9.38e-02 | -2.846 | ribonucleoside-diphosphate reductase small chain, putative | NA |
| 511 | PF3D7_1410000 | Pf3D7_14_v3 | 392972 | - | 879 | 0.428 | -0.401 | 1.257 | 6.119 | 2.608 | 1.27e-02 | 9.46e-02 | -3.248 | ER membrane protein complex subunit 2, putative | EMC2 |
| 47 | PF3D7_0318900 | Pf3D7_03_v3 | 791840 | - | 1642 | -0.368 | -1.187 | 0.450 | 5.696 | -2.605 | 1.28e-02 | 9.47e-02 | -3.206 | conserved protein, unknown function | NA |
| 196 | PF3D7_0724300 | Pf3D7_07_v3 | 1021508 | + | 1123 | 0.774 | 0.112 | 1.437 | 1.018 | 2.604 | 1.28e-02 | 9.47e-02 | -2.873 | 3-demethylubiquinone-9 3-methyltransferase, putative | COQ3 |
| 251 | PF3D7_0914300 | Pf3D7_09_v3 | 612976 | - | 2517 | 0.367 | -0.685 | 1.419 | 6.852 | 2.606 | 1.28e-02 | 9.47e-02 | -3.314 | met-10+ like protein, putative | NA |
| 388 | PF3D7_1223300 | Pf3D7_12_v3 | 934971 | - | 3669 | 0.474 | -0.391 | 1.339 | 4.880 | 2.605 | 1.28e-02 | 9.47e-02 | -3.115 | DNA gyrase subunit A | GyrA |
| 259 | PF3D7_0923000 | Pf3D7_09_v3 | 939580 | - | 1008 | 0.392 | -0.117 | 0.900 | 6.135 | 2.603 | 1.28e-02 | 9.47e-02 | -3.251 | DNA-directed RNA polymerase II subunit RPB3, putative | RPB3 |
| 38 | PF3D7_0308900 | Pf3D7_03_v3 | 379130 | - | 4161 | -0.402 | -0.629 | -0.176 | 8.929 | -2.602 | 1.29e-02 | 9.50e-02 | -3.419 | splicing factor 3B subunit 1, putative | SF3B1 |
| 219 | PF3D7_0820800 | Pf3D7_08_v3 | 936426 | - | 2451 | 0.882 | 0.384 | 1.379 | 0.753 | 2.598 | 1.30e-02 | 9.54e-02 | -2.875 | conserved Plasmodium protein, unknown function | NA |
| 242 | PF3D7_0905800 | Pf3D7_09_v3 | 289050 | + | 3848 | 0.418 | -1.178 | 2.014 | 6.548 | 2.599 | 1.30e-02 | 9.54e-02 | -3.297 | conserved Plasmodium protein, unknown function | NA |
| 102 | PF3D7_0516600 | Pf3D7_05_v3 | 686810 | - | 4833 | 0.775 | 0.169 | 1.382 | 5.100 | 2.594 | 1.32e-02 | 9.57e-02 | -3.149 | sporozoite surface antigen MB2 | MB2 |
| 115 | PF3D7_0522800 | Pf3D7_05_v3 | 944184 | - | 748 | -0.415 | -0.745 | -0.085 | 6.133 | -2.594 | 1.31e-02 | 9.57e-02 | -3.268 | pre-mRNA-splicing factor BUD31, putative | BUD31 |
| 140 | PF3D7_0608200 | Pf3D7_06_v3 | 341874 | - | 948 | -0.767 | -1.230 | -0.303 | 1.094 | -2.593 | 1.32e-02 | 9.57e-02 | -2.896 | conserved Plasmodium protein, unknown function | NA |
| 158 | PF3D7_0628700 | Pf3D7_06_v3 | 1183896 | + | 1722 | 0.654 | 0.331 | 0.978 | 2.910 | 2.592 | 1.32e-02 | 9.57e-02 | -2.973 | conserved Plasmodium protein, unknown function | NA |
| 224 | PF3D7_0822500 | Pf3D7_08_v3 | 992655 | - | 1311 | 0.743 | 0.249 | 1.236 | 3.613 | 2.596 | 1.31e-02 | 9.57e-02 | -3.013 | dynein light chain 1 | DLC1 |
| 356 | PF3D7_1139700 | Pf3D7_11_v3 | 1582995 | - | 1518 | 0.857 | 0.217 | 1.498 | 0.400 | 2.593 | 1.32e-02 | 9.57e-02 | -2.879 | adrenodoxin reductase, putative | NA |
| 521 | PF3D7_1417200 | Pf3D7_14_v3 | 694585 | + | 13593 | -0.389 | -0.834 | 0.055 | 9.868 | -2.592 | 1.32e-02 | 9.57e-02 | -3.451 | NOT family protein, putative | NA |
| 50 | PF3D7_0319900 | Pf3D7_03_v3 | 833833 | - | 945 | 0.660 | 0.179 | 1.142 | 3.869 | 2.590 | 1.33e-02 | 9.57e-02 | -3.053 | conserved Plasmodium protein, unknown function | NA |
| 320 | PF3D7_1104800 | Pf3D7_11_v3 | 207440 | + | 2293 | -0.691 | -1.339 | -0.042 | 3.529 | -2.590 | 1.33e-02 | 9.57e-02 | -3.089 | metabolite/drug transporter, putative | NA |
| 425 | PF3D7_1250900 | Pf3D7_12_v3 | 2083353 | - | 966 | 0.877 | -0.398 | 2.153 | 1.962 | 2.589 | 1.33e-02 | 9.57e-02 | -2.934 | conserved Plasmodium protein, unknown function | NA |
| 456 | PF3D7_1327600 | Pf3D7_13_v3 | 1159366 | + | 615 | 0.947 | -0.145 | 2.039 | 2.094 | 2.591 | 1.33e-02 | 9.57e-02 | -2.935 | nicotinate-nucleotide adenylyltransferase | NMNAT |
| 20 | PF3D7_0208300 | Pf3D7_02_v3 | 337558 | + | 5409 | 0.654 | -0.021 | 1.329 | 4.892 | 2.582 | 1.36e-02 | 9.74e-02 | -3.174 | conserved Plasmodium protein, unknown function | NA |
| 111 | PF3D7_0520400 | Pf3D7_05_v3 | 839655 | - | 906 | 0.813 | 0.084 | 1.542 | 2.273 | 2.580 | 1.36e-02 | 9.74e-02 | -2.965 | conserved Plasmodium protein, unknown function | NA |
| 458 | PF3D7_1330700 | Pf3D7_13_v3 | 1290118 | + | 2837 | 0.982 | 0.075 | 1.890 | 0.959 | 2.580 | 1.36e-02 | 9.74e-02 | -2.919 | GPI transamidase subunit PIG-U, putative | NA |
| 476 | PF3D7_1350300 | Pf3D7_13_v3 | 2011168 | + | 918 | -0.573 | -1.138 | -0.008 | 5.457 | -2.575 | 1.38e-02 | 9.85e-02 | -3.230 | conserved Plasmodium protein, unknown function | NA |
| 21 | PF3D7_0208400 | Pf3D7_02_v3 | 343308 | - | 6033 | -0.376 | -0.892 | 0.140 | 6.534 | -2.573 | 1.39e-02 | 9.88e-02 | -3.360 | conserved Plasmodium protein, unknown function | NA |
| 41 | PF3D7_0314400 | Pf3D7_03_v3 | 579539 | - | 927 | -0.535 | -1.108 | 0.039 | 5.825 | -2.568 | 1.40e-02 | 9.91e-02 | -3.313 | serine/threonine protein phosphatase 6, putative | PPP6 |
| 42 | PF3D7_0315800 | Pf3D7_03_v3 | 641482 | - | 1098 | 0.457 | -0.449 | 1.363 | 5.708 | 2.570 | 1.40e-02 | 9.91e-02 | -3.281 | zinc finger protein, putative | NA |
| 210 | PF3D7_0811100 | Pf3D7_08_v3 | 557884 | - | 1623 | 0.946 | 0.129 | 1.762 | 0.493 | 2.570 | 1.40e-02 | 9.91e-02 | -2.931 | mitochondrial carrier protein, putative | NA |
| 463 | PF3D7_1336200 | Pf3D7_13_v3 | 1474274 | + | 1388 | -1.121 | -1.435 | -0.807 | 1.096 | -2.569 | 1.40e-02 | 9.91e-02 | -2.944 | conserved Plasmodium protein, unknown function | NA |
| 577 | PF3D7_1467500 | Pf3D7_14_v3 | 2755225 | + | 1575 | -0.339 | -0.746 | 0.067 | 6.555 | -2.568 | 1.40e-02 | 9.91e-02 | -3.373 | DNA/RNA-binding protein KIN17, putative | NA |
col_annot <- data.frame(row.names = colnames(v$E), stringsAsFactors = F)
col_annot$phenotype[substring(colnames(v$E), 1, 1) == "I"] <- "non-severe"
col_annot$phenotype[substring(colnames(v$E), 1, 1) == "S"] <- "severe"
col_annot$phenotype <- as.factor(col_annot$phenotype)
pheatmap(v2$E[rownames(v$E) %in% top_ring_ruv$GeneID, ], show_rownames = FALSE, scale = "row", annotation_col = col_annot, annotation_colors = list(phenotype = c(`non-severe` = colors[1],
severe = colors[2])))
We now test using roast and camera for deregulation of gene sets obtained from the papers:
Daily, J. P., D. Scanfeld, N. Pochet, K. Le Roch, D. Plouffe, M. Kamal, O. Sarr, et al. 2007. “Distinct Physiological States of Plasmodium Falciparum in Malaria-Infected Patients.” Nature 450 (7172): 1091–95.
Shock, Jennifer L., Kael F. Fischer, and Joseph L. DeRisi. 2007. “Whole-Genome Analysis of mRNA Decay in Plasmodium Falciparum Reveals a Global Lengthening of mRNA Half-Life during the Intra-Erythrocytic Development Cycle.” Genome Biology 8 (7): R134.
setwd(wd)
# Load gene lists from Daily et al and Shock et al
daily_figure2 <- fread("./data/daily_expression_figure2.csv", data.table = FALSE, header = TRUE)
JLshock <- c("PF3D7_0320800", "PF3D7_0410400", "PF3D7_0507600", "PF3D7_0520300", "PF3D7_0720000", "PF3D7_0811300", "PF3D7_0819900", "PF3D7_0909400", "PF3D7_0909900",
"PF3D7_1006100", "PF3D7_1032100", "PF3D7_1103800", "PF3D7_1106300", "PF3D7_1107000", "PF3D7_1124400", "PF3D7_1128600", "PF3D7_1209200", "PF3D7_1224300",
"PF3D7_1235300", "PF3D7_1307000", "PF3D7_1308900", "PF3D7_1325000", "PF3D7_1340100", "PF3D7_1364500", "PF3D7_1427800", "PF3D7_1443300", "PF3D7_1443500",
"PF3D7_1449700", "PF3D7_0519500")
# Load entrex geneID mappings
entrez_geneID_mappings <- fread("./data/geneID_mappings.txt", data.table = FALSE, stringsAsFactors = FALSE)
upcluster2 <- daily_figure2$Gene[daily_figure2$`Up regulated in Cluster 2?` == "Y"]
upcluster1 <- daily_figure2$Gene[daily_figure2$`Up regulated in Cluster 2?` == "N"]
glycolisis <- daily_figure2$Gene[daily_figure2$type == "Glycolisis"]
tricarboxylic <- daily_figure2$Gene[daily_figure2$type == "Tricarboxylic acid cycle"]
fatty_acid <- daily_figure2$Gene[daily_figure2$type == "Fatty acid metabolism"]
upcluster2 <- as.vector(geneID_mappings$current[geneID_mappings$old %in% upcluster2])
upcluster1 <- as.vector(geneID_mappings$current[geneID_mappings$old %in% upcluster1])
glycolisis <- as.vector(geneID_mappings$current[geneID_mappings$old %in% glycolisis])
tricarboxylic <- as.vector(geneID_mappings$current[geneID_mappings$old %in% tricarboxylic])
fatty_acid <- as.vector(geneID_mappings$current[geneID_mappings$old %in% fatty_acid])
indices <- ids2indices(list(up_in_starvation = upcluster1, up_int_vitro = upcluster2, glycolisis = glycolisis, tricarboxylic = tricarboxylic, fatty_acid = fatty_acid,
mRNA_degradation = JLshock), rownames(v2$E))
mroast(v2, index = indices, design = modRUV, contrast = 2, nrot = 10000, set.statistic = "floormean")
## NGenes PropDown PropUp Direction PValue FDR PValue.Mixed FDR.Mixed
## mRNA_degradation 29 0.2758621 0.06896552 Down 0.00629937 0.02204780 0.00129987 0.004649535
## up_int_vitro 12 0.8333333 0.00000000 Down 0.00739926 0.02204780 0.00789921 0.011773823
## tricarboxylic 11 0.1818182 0.36363636 Up 0.01219878 0.02422258 0.00159984 0.004649535
## glycolisis 19 0.5263158 0.00000000 Down 0.01619838 0.02422258 0.01509849 0.015098490
## up_in_starvation 33 0.1515152 0.21212121 Up 0.03609639 0.04325567 0.00329967 0.006499350
## fatty_acid 17 0.1764706 0.17647059 Up 0.06279372 0.06279372 0.01259874 0.015048495
camera(v2, index = indices, design = modRUV, contrast = 2)
## NGenes Correlation Direction PValue FDR
## up_int_vitro 12 0.55011389 Down 0.1013887 0.4438285
## glycolisis 19 0.24854294 Down 0.1593857 0.4438285
## mRNA_degradation 29 0.06758603 Down 0.2219142 0.4438285
## tricarboxylic 11 0.06650577 Up 0.3661151 0.4725657
## up_in_starvation 33 0.07007488 Up 0.4263498 0.4725657
## fatty_acid 17 0.05459497 Up 0.4725657 0.4725657
# setwd(wd) entrez_de <- entrez_geneID_mappings$`[Entrez Gene ID]`[entrez_geneID_mappings$`[Gene ID]` %in% top_ring_ruv$GeneID] entrez_de <-
# entrez_de[entrez_de!='null'] entrez_de <- str_split_fixed(entrez_de, pattern = ',', n = 2)[,1] kegg <- kegga(entrez_de, species.KEGG='pfa',
# convert=TRUE) kable(topKEGG(kegg, n=Inf))
# go <- goana(entrez_de, species.KEGG='pfa', convert=TRUE) kable(topGO(go, n=100))
setwd(wd)
sessionInfo()
## R version 3.2.0 (2015-04-16)
## Platform: x86_64-apple-darwin15.4.0 (64-bit)
## Running under: OS X 10.11.4 (unknown)
##
## locale:
## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
##
## attached base packages:
## [1] grid stats4 parallel stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] pheatmap_1.0.8 knitr_1.15.1 stringr_1.1.0 dplyr_0.5.0 data.table_1.10.0
## [6] VennDiagram_1.6.17 futile.logger_1.4.3 RColorBrewer_1.1-2 EDASeq_2.4.1 ShortRead_1.28.0
## [11] GenomicAlignments_1.6.3 SummarizedExperiment_1.0.2 Rsamtools_1.22.0 GenomicRanges_1.22.4 GenomeInfoDb_1.6.3
## [16] Biostrings_2.38.4 XVector_0.10.0 IRanges_2.4.8 S4Vectors_0.8.11 BiocParallel_1.4.3
## [21] Biobase_2.30.0 BiocGenerics_0.16.1 reshape2_1.4.2 ggplot2_2.2.1 ruv_0.9.6
## [26] quadprog_1.5-5 edgeR_3.12.1 limma_3.26.9
##
## loaded via a namespace (and not attached):
## [1] splines_3.2.0 R.utils_2.5.0 assertthat_0.1 statmod_1.4.27 highr_0.6 aroma.light_3.0.0
## [7] latticeExtra_0.6-28 yaml_2.1.14 RSQLite_1.1-1 backports_1.0.4 lattice_0.20-31 digest_0.6.11
## [13] colorspace_1.3-2 htmltools_0.3.5 Matrix_1.2-0 R.oo_1.21.0 plyr_1.8.4 XML_3.98-1.5
## [19] biomaRt_2.26.1 genefilter_1.52.1 zlibbioc_1.16.0 xtable_1.8-2 scales_0.4.1 tibble_1.2
## [25] annotate_1.48.0 GenomicFeatures_1.22.13 lazyeval_0.2.0 survival_2.40-1 magrittr_1.5 memoise_1.0.0
## [31] evaluate_0.10 R.methodsS3_1.7.1 hwriter_1.3.2 tools_3.2.0 formatR_1.4 matrixStats_0.51.0
## [37] munsell_0.4.3 AnnotationDbi_1.32.3 lambda.r_1.1.9 DESeq_1.22.1 RCurl_1.95-4.8 bitops_1.0-6
## [43] labeling_0.3 rmarkdown_1.3 gtable_0.2.0 DBI_0.5-1 R6_2.2.0 rtracklayer_1.30.4
## [49] rprojroot_1.1 futile.options_1.0.0 stringi_1.1.2 Rcpp_0.12.8 geneplotter_1.48.0